STAR compilation error
#1503
Replies: 10 comments
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Hi Werner, have you tried to run the compiled executable Best, |
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Hi Alex,
many thanks for getting back to me!
yes, I have tried the compiled version - same issue.
however, I was able to run the STAR indexing successfully (I think) on the server.
unfortunately, now I am getting a weird error message for the genomeParameters.txt file created during indexing when I run the STAR alignment (on the server):
"unrecoginzed parameter name "genomeType" in input "genomeParameters.txt"
looking online people seem to get this error when using different versions of STAR for indexing and alignment.
however, I used the most uptodate version of STAR on our server (2.7.9a) for both.
the ‘versionGenome 2.7.4a’ line in genomeParameters.txt confused me initially but it seems to list the earliest version of STAR to be compatible with the index file not the version it was created with.
is this an issue with the latest version of STAR and should I redo this with an earlier version?
I attached the script and log files for reference.
Many thanks, Werner
——————SCRIPT for STAR alignment on input file: STAR_alignment_on_input_file.sh
#!/bin/bash/
# This script takes a fastq file of RNA-seq data, runs STAR alignment
# USAGE: sh STAR_alignment_on_input_file.sh <name of fastq file>
# output directory: /n/scratch3/users/w/wn19/results/STAR
# make sure gcc, star are installed and in $PATH
module load gcc/6.2.0 star/2.7.9a
export PATH=/n/app/bcbio/dev/anaconda/bin:$PATH
# change directories to /n/scratch2/ so that all the analysis is stored there.
cd /n/scratch3/users/w/wn19/results/STAR/
# initialize a variable with an intuitive name to store the name of the input fastq file
fq=$1
# grab base of filename for naming outputs
base=`basename $fq .sample.fastq`
echo "Sample name is $base"
# specify the number of cores to use- provides an easy way to modify the script to run with more or fewer cores without have to replace the number within all commands where cores are specified
cores=20
#initialize a variable named genome with the path to the STAR genome index file
genome=/n/scratch3/users/w/wn19/hg38_index
# set up variable with paths to output filenames and locations
align_out=/n/scratch3/users/w/wn19/results/STAR/${base}_
align_out_bam=/n/scratch3/users/w/wn19/results/STAR/${base}_Aligned.sortedByCoord.out.bam
#Preparing for future debugging
echo "Processing file $fq"
# Run STAR
STAR --genomeDir $genome --readFilesIn $fq --outFileNamePrefix $align_out --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard
——————END SCRIPT
———————————————— SCRIPT: STAR all files in parallel: STAR_alignment_on_allfiles_parallel_for_slurm.test.sh
#! /bin/bash
for fq in /n/scratch3/users/w/wn19/PREP0166_sample_test/*.sample.fastq
do
sbatch -p short -t 0-0:15 -c 20 --job-name STAR_alignment_RNAseq --mem 64G --wrap="sh /home/wn19/scripts/STAR_alignment_on_input_file.sh $fq"
sleep 1 # wait 1 second between each job submission
done
——————— END SCRIPT
On Mar 14, 2022, at 5:44 PM, Alexander Dobin ***@***.***> wrote:
Hi Werner,
have you tried to run the compiled executable bin/MacOSX_x86_64/STAR?
This might be easier than compiling it.
Best,
Alex
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You are receiving this because you authored the thread.
### STAR --runMode genomeGenerate --runThreadN 20 --genomeDir /n/scratch3/users/w/wn19/hg38_index --genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf --sjdbOverhang 99
### GstrandBit 32
versionGenome 2.7.4a
genomeType Full
genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeTransformType None
genomeTransformVCF -
sjdbOverhang 99
sjdbFileChrStartEnd -
sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbInsertSave Basic
genomeFileSizes 3216987595 24948435851
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Hi Werner, |
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Hi Alex,
I had attached them to the previous email.
I am also pasting them below into this email in case the attachments did not come through.
Many thanks!
…------------------------------------------
MAPPING log.out
***@***.*** STAR]$ view PREP0162_WNeuhREA12700A_A01v1_RNA_16c_S1.R1_Log.out
chimMultimapNmax 0
chimMultimapScoreRange 1
chimNonchimScoreDropMin 20
chimOutJunctionFormat 0
sjdbFileChrStartEnd -
sjdbGTFfile -
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbOverhang 100
sjdbScore 2
sjdbInsertSave Basic
varVCFfile -
waspOutputMode None
quantMode -
quantTranscriptomeBAMcompression 1
quantTranscriptomeBan IndelSoftclipSingleend
twopass1readsN 18446744073709551615
twopassMode None
----------------------------------------
WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting
Finished loading and checking parameters
Reading genome generation parameters:
### STAR --runMode genomeGenerate --runThreadN 20 --genomeDir /n/scratch3/users/w/wn19/hg38_index --genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf --sjdbOverhang 99
### GstrandBit=32
versionGenome 2 0 ~RE-DEFINED
EXITING: FATAL INPUT ERROR: unrecoginzed parameter name "genomeType" in input "genomeParameters.txt"
SOLUTION: use correct parameter name (check the manual)
Mar 14 15:29:01 ...... FATAL ERROR, exiting
————————————
INDEXING log.out
STAR version=2.7.9a
STAR compilation time,server,dir=2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
##### Command Line:
STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /n/scratch3/users/w/wn19/hg38_index --genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf --sjdbOverhang 99
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runThreadN 20 ~RE-DEFINED
runMode genomeGenerate ~RE-DEFINED
genomeDir /n/scratch3/users/w/wn19/hg38_index ~RE-DEFINED
genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa ~RE-DEFINED
sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf ~RE-DEFINED
sjdbOverhang 99 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runMode genomeGenerate
runThreadN 20
genomeDir /n/scratch3/users/w/wn19/hg38_index
genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa
sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf
sjdbOverhang 99
-------------------------------
##### Final effective command line:
STAR --runMode genomeGenerate --runThreadN 20 --genomeDir /n/scratch3/users/w/wn19/hg38_index --genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf --sjdbOverhang 99
----------------------------------------
Number of fastq files for each mate = 1
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters: 3000 0.99 10
Finished loading and checking parameters
--genomeDir directory created: /n/scratch3/users/w/wn19/hg38_index/
!!!!! WARNING: Could not move Log.out file from ./Log.out into /n/scratch3/users/w/wn19/hg38_index/Log.out. Will keep ./Log.out
Mar 11 14:31:25 ... starting to generate Genome files
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 0 "1" chrStart: 0
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 1 "10" chrStart: 249036800
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 2 "11" chrStart: 382992384
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 3 "12" chrStart: 518258688
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 4 "13" chrStart: 651689984
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 5 "14" chrStart: 766246912
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 6 "15" chrStart: 873463808
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 7 "16" chrStart: 975699968
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 8 "17" chrStart: 1066139648
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 9 "18" chrStart: 1149501440
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 10 "19" chrStart: 1229979648
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 11 "2" chrStart: 1288699904
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 12 "20" chrStart: 1530920960
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 13 "21" chrStart: 1595408384
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 14 "22" chrStart: 1642332160
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 15 "3" chrStart: 1693188096
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 16 "4" chrStart: 1891631104
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 17 "5" chrStart: 2081947648
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 18 "6" chrStart: 2263613440
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 19 "7" chrStart: 2434531328
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 20 "8" chrStart: 2593914880
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 21 "9" chrStart: 2739142656
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 22 "MT" chrStart: 2877554688
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 23 "X" chrStart: 2877816832
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 24 "Y" chrStart: 3034054656
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 25 "KI270728.1" chrStart: 3091464192
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 26 "KI270727.1" chrStart: 3093561344
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 27 "KI270442.1" chrStart: 3094085632
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 28 "KI270729.1" chrStart: 3094609920
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 29 "GL000225.1" chrStart: 3095134208
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 30 "KI270743.1" chrStart: 3095396352
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 31 "GL000008.2" chrStart: 3095658496
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 32 "GL000009.2" chrStart: 3095920640
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 33 "KI270747.1" chrStart: 3096182784
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 34 "KI270722.1" chrStart: 3096444928
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 35 "GL000194.1" chrStart: 3096707072
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 36 "KI270742.1" chrStart: 3096969216
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 37 "GL000205.2" chrStart: 3097231360
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 38 "GL000195.1" chrStart: 3097493504
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 39 "KI270736.1" chrStart: 3097755648
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 40 "KI270733.1" chrStart: 3098017792
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 41 "GL000224.1" chrStart: 3098279936
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 42 "GL000219.1" chrStart: 3098542080
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 43 "KI270719.1" chrStart: 3098804224
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 44 "GL000216.2" chrStart: 3099066368
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 45 "KI270712.1" chrStart: 3099328512
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 46 "KI270706.1" chrStart: 3099590656
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 47 "KI270725.1" chrStart: 3099852800
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 48 "KI270744.1" chrStart: 3100114944
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 49 "KI270734.1" chrStart: 3100377088
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 50 "GL000213.1" chrStart: 3100639232
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 51 "GL000220.1" chrStart: 3100901376
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 52 "KI270715.1" chrStart: 3101163520
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 53 "GL000218.1" chrStart: 3101425664
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 54 "KI270749.1" chrStart: 3101687808
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 55 "KI270741.1" chrStart: 3101949952
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 56 "GL000221.1" chrStart: 3102212096
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 57 "KI270716.1" chrStart: 3102474240
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 58 "KI270731.1" chrStart: 3102736384
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 59 "KI270751.1" chrStart: 3102998528
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 60 "KI270750.1" chrStart: 3103260672
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 61 "KI270519.1" chrStart: 3103522816
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 62 "GL000214.1" chrStart: 3103784960
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 63 "KI270708.1" chrStart: 3104047104
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 64 "KI270730.1" chrStart: 3104309248
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 65 "KI270438.1" chrStart: 3104571392
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 66 "KI270737.1" chrStart: 3104833536
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 67 "KI270721.1" chrStart: 3105095680
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 68 "KI270738.1" chrStart: 3105357824
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 69 "KI270748.1" chrStart: 3105619968
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 70 "KI270435.1" chrStart: 3105882112
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 71 "GL000208.1" chrStart: 3106144256
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 72 "KI270538.1" chrStart: 3106406400
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 73 "KI270756.1" chrStart: 3106668544
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 74 "KI270739.1" chrStart: 3106930688
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 75 "KI270757.1" chrStart: 3107192832
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 76 "KI270709.1" chrStart: 3107454976
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 77 "KI270746.1" chrStart: 3107717120
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 78 "KI270753.1" chrStart: 3107979264
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 79 "KI270589.1" chrStart: 3108241408
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 80 "KI270726.1" chrStart: 3108503552
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 81 "KI270735.1" chrStart: 3108765696
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 82 "KI270711.1" chrStart: 3109027840
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 83 "KI270745.1" chrStart: 3109289984
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 84 "KI270714.1" chrStart: 3109552128
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 85 "KI270732.1" chrStart: 3109814272
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 86 "KI270713.1" chrStart: 3110076416
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 87 "KI270754.1" chrStart: 3110338560
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 88 "KI270710.1" chrStart: 3110600704
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 89 "KI270717.1" chrStart: 3110862848
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 90 "KI270724.1" chrStart: 3111124992
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 91 "KI270720.1" chrStart: 3111387136
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 92 "KI270723.1" chrStart: 3111649280
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 93 "KI270718.1" chrStart: 3111911424
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 94 "KI270317.1" chrStart: 3112173568
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 95 "KI270740.1" chrStart: 3112435712
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 96 "KI270755.1" chrStart: 3112697856
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 97 "KI270707.1" chrStart: 3112960000
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 98 "KI270579.1" chrStart: 3113222144
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 99 "KI270752.1" chrStart: 3113484288
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 100 "KI270512.1" chrStart: 3113746432
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 101 "KI270322.1" chrStart: 3114008576
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 102 "GL000226.1" chrStart: 3114270720
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 103 "KI270311.1" chrStart: 3114532864
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 104 "KI270366.1" chrStart: 3114795008
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 105 "KI270511.1" chrStart: 3115057152
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 106 "KI270448.1" chrStart: 3115319296
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 107 "KI270521.1" chrStart: 3115581440
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 108 "KI270581.1" chrStart: 3115843584
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 109 "KI270582.1" chrStart: 3116105728
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 110 "KI270515.1" chrStart: 3116367872
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 111 "KI270588.1" chrStart: 3116630016
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 112 "KI270591.1" chrStart: 3116892160
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 113 "KI270522.1" chrStart: 3117154304
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 114 "KI270507.1" chrStart: 3117416448
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 115 "KI270590.1" chrStart: 3117678592
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 116 "KI270584.1" chrStart: 3117940736
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 117 "KI270320.1" chrStart: 3118202880
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 118 "KI270382.1" chrStart: 3118465024
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 119 "KI270468.1" chrStart: 3118727168
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 120 "KI270467.1" chrStart: 3118989312
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 121 "KI270362.1" chrStart: 3119251456
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 122 "KI270517.1" chrStart: 3119513600
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 123 "KI270593.1" chrStart: 3119775744
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 124 "KI270528.1" chrStart: 3120037888
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 125 "KI270587.1" chrStart: 3120300032
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 126 "KI270364.1" chrStart: 3120562176
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 127 "KI270371.1" chrStart: 3120824320
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 128 "KI270333.1" chrStart: 3121086464
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 129 "KI270374.1" chrStart: 3121348608
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 130 "KI270411.1" chrStart: 3121610752
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 131 "KI270414.1" chrStart: 3121872896
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 132 "KI270510.1" chrStart: 3122135040
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 133 "KI270390.1" chrStart: 3122397184
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 134 "KI270375.1" chrStart: 3122659328
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 135 "KI270420.1" chrStart: 3122921472
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 136 "KI270509.1" chrStart: 3123183616
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 137 "KI270315.1" chrStart: 3123445760
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 138 "KI270302.1" chrStart: 3123707904
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 139 "KI270518.1" chrStart: 3123970048
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 140 "KI270530.1" chrStart: 3124232192
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 141 "KI270304.1" chrStart: 3124494336
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 142 "KI270418.1" chrStart: 3124756480
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 143 "KI270424.1" chrStart: 3125018624
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 144 "KI270417.1" chrStart: 3125280768
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 145 "KI270508.1" chrStart: 3125542912
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 146 "KI270303.1" chrStart: 3125805056
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 147 "KI270381.1" chrStart: 3126067200
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 148 "KI270529.1" chrStart: 3126329344
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 149 "KI270425.1" chrStart: 3126591488
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 150 "KI270396.1" chrStart: 3126853632
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 151 "KI270363.1" chrStart: 3127115776
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 152 "KI270386.1" chrStart: 3127377920
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 153 "KI270465.1" chrStart: 3127640064
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 154 "KI270383.1" chrStart: 3127902208
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 155 "KI270384.1" chrStart: 3128164352
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 156 "KI270330.1" chrStart: 3128426496
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 157 "KI270372.1" chrStart: 3128688640
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 158 "KI270548.1" chrStart: 3128950784
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 159 "KI270580.1" chrStart: 3129212928
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 160 "KI270387.1" chrStart: 3129475072
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 161 "KI270391.1" chrStart: 3129737216
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 162 "KI270305.1" chrStart: 3129999360
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 163 "KI270373.1" chrStart: 3130261504
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 164 "KI270422.1" chrStart: 3130523648
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 165 "KI270316.1" chrStart: 3130785792
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 166 "KI270340.1" chrStart: 3131047936
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 167 "KI270338.1" chrStart: 3131310080
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 168 "KI270583.1" chrStart: 3131572224
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 169 "KI270334.1" chrStart: 3131834368
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 170 "KI270429.1" chrStart: 3132096512
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 171 "KI270393.1" chrStart: 3132358656
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 172 "KI270516.1" chrStart: 3132620800
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 173 "KI270389.1" chrStart: 3132882944
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 174 "KI270466.1" chrStart: 3133145088
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 175 "KI270388.1" chrStart: 3133407232
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 176 "KI270544.1" chrStart: 3133669376
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 177 "KI270310.1" chrStart: 3133931520
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 178 "KI270412.1" chrStart: 3134193664
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 179 "KI270395.1" chrStart: 3134455808
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 180 "KI270376.1" chrStart: 3134717952
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 181 "KI270337.1" chrStart: 3134980096
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 182 "KI270335.1" chrStart: 3135242240
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 183 "KI270378.1" chrStart: 3135504384
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 184 "KI270379.1" chrStart: 3135766528
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 185 "KI270329.1" chrStart: 3136028672
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 186 "KI270419.1" chrStart: 3136290816
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 187 "KI270336.1" chrStart: 3136552960
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 188 "KI270312.1" chrStart: 3136815104
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 189 "KI270539.1" chrStart: 3137077248
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 190 "KI270385.1" chrStart: 3137339392
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 191 "KI270423.1" chrStart: 3137601536
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 192 "KI270392.1" chrStart: 3137863680
/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa : chr # 193 "KI270394.1" chrStart: 3138125824
Chromosome sequence lengths:
1 248956422
10 133797422
11 135086622
12 133275309
13 114364328
14 107043718
15 101991189
16 90338345
17 83257441
18 80373285
19 58617616
2 242193529
20 64444167
21 46709983
22 50818468
3 198295559
4 190214555
5 181538259
6 170805979
7 159345973
8 145138636
9 138394717
MT 16569
X 156040895
Y 57227415
KI270728.1 1872759
KI270727.1 448248
KI270442.1 392061
KI270729.1 280839
GL000225.1 211173
KI270743.1 210658
GL000008.2 209709
GL000009.2 201709
KI270747.1 198735
KI270722.1 194050
GL000194.1 191469
KI270742.1 186739
GL000205.2 185591
GL000195.1 182896
KI270736.1 181920
KI270733.1 179772
GL000224.1 179693
GL000219.1 179198
KI270719.1 176845
GL000216.2 176608
KI270712.1 176043
KI270706.1 175055
KI270725.1 172810
KI270744.1 168472
KI270734.1 165050
GL000213.1 164239
GL000220.1 161802
KI270715.1 161471
GL000218.1 161147
KI270749.1 158759
KI270741.1 157432
GL000221.1 155397
KI270716.1 153799
KI270731.1 150754
KI270751.1 150742
KI270750.1 148850
KI270519.1 138126
GL000214.1 137718
KI270708.1 127682
KI270730.1 112551
KI270438.1 112505
KI270737.1 103838
KI270721.1 100316
KI270738.1 99375
KI270748.1 93321
KI270435.1 92983
GL000208.1 92689
KI270538.1 91309
KI270756.1 79590
KI270739.1 73985
KI270757.1 71251
KI270709.1 66860
KI270746.1 66486
KI270753.1 62944
KI270589.1 44474
KI270726.1 43739
KI270735.1 42811
KI270711.1 42210
KI270745.1 41891
KI270714.1 41717
KI270732.1 41543
KI270713.1 40745
KI270754.1 40191
KI270710.1 40176
KI270717.1 40062
KI270724.1 39555
KI270720.1 39050
KI270723.1 38115
KI270718.1 38054
KI270317.1 37690
KI270740.1 37240
KI270755.1 36723
KI270707.1 32032
KI270579.1 31033
KI270752.1 27745
KI270512.1 22689
KI270322.1 21476
GL000226.1 15008
KI270311.1 12399
KI270366.1 8320
KI270511.1 8127
KI270448.1 7992
KI270521.1 7642
KI270581.1 7046
KI270582.1 6504
KI270515.1 6361
KI270588.1 6158
KI270591.1 5796
KI270522.1 5674
KI270507.1 5353
KI270590.1 4685
KI270584.1 4513
KI270320.1 4416
KI270382.1 4215
KI270468.1 4055
KI270467.1 3920
KI270362.1 3530
KI270517.1 3253
KI270593.1 3041
KI270528.1 2983
KI270587.1 2969
KI270364.1 2855
KI270371.1 2805
KI270333.1 2699
KI270374.1 2656
KI270411.1 2646
KI270414.1 2489
KI270510.1 2415
KI270390.1 2387
KI270375.1 2378
KI270420.1 2321
KI270509.1 2318
KI270315.1 2276
KI270302.1 2274
KI270518.1 2186
KI270530.1 2168
KI270304.1 2165
KI270418.1 2145
KI270424.1 2140
KI270417.1 2043
KI270508.1 1951
KI270303.1 1942
KI270381.1 1930
KI270529.1 1899
KI270425.1 1884
KI270396.1 1880
KI270363.1 1803
KI270386.1 1788
KI270465.1 1774
KI270383.1 1750
KI270384.1 1658
KI270330.1 1652
KI270372.1 1650
KI270548.1 1599
KI270580.1 1553
KI270387.1 1537
KI270391.1 1484
KI270305.1 1472
KI270373.1 1451
KI270422.1 1445
KI270316.1 1444
KI270340.1 1428
KI270338.1 1428
KI270583.1 1400
KI270334.1 1368
KI270429.1 1361
KI270393.1 1308
KI270516.1 1300
KI270389.1 1298
KI270466.1 1233
KI270388.1 1216
KI270544.1 1202
KI270310.1 1201
KI270412.1 1179
KI270395.1 1143
KI270376.1 1136
KI270337.1 1121
KI270335.1 1048
KI270378.1 1048
KI270379.1 1045
KI270329.1 1040
KI270419.1 1029
KI270336.1 1026
KI270312.1 998
KI270539.1 993
KI270385.1 990
KI270423.1 981
KI270392.1 971
KI270394.1 970
Genome sequence total length = 3099750718
Genome size with padding = 3138387968
Mar 11 14:32:24 ..... processing annotations GTF
Processing pGe.sjdbGTFfile=/home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf, found:
244825 transcripts
1552026 exons (non-collapsed)
395016 collapsed junctions
Total junctions: 395016
Mar 11 14:32:43 ..... finished GTF processing
Estimated genome size with padding and SJs: total=genome+SJ=3337387968 = 3138387968 + 199000000
GstrandBit=32
Number of SA indices: 5891698134
Mar 11 14:32:59 ... starting to sort Suffix Array. This may take a long time...
Number of chunks: 73; chunks size limit: 741696712 bytes
Mar 11 14:33:18 ... sorting Suffix Array chunks and saving them to disk...
Writing 473008240 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_2 ; empty space on disk = 557764535386112 bytes ... done
Writing 473125624 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_6 ; empty space on disk = 557708902137856 bytes ... done
Writing 645538840 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_14 ; empty space on disk = 557669710561280 bytes ... done
Writing 528233960 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_10 ; empty space on disk = 557669710561280 bytes ... done
Writing 618627792 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_19 ; empty space on disk = 557658704707584 bytes ... done
Writing 725537968 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_0 ; empty space on disk = 557606804389888 bytes ... done
Writing 612296224 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_7 ; empty space on disk = 557606804389888 bytes ... done
Writing 655512152 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_13 ; empty space on disk = 557606804389888 bytes ... done
Writing 581718384 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_5 ; empty space on disk = 557646398619648 bytes ... done
Writing 663827040 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_9 ; empty space on disk = 557646398619648 bytes ... done
Writing 721019080 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_15 ; empty space on disk = 557623514497024 bytes ... done
Writing 656158256 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_18 ; empty space on disk = 557609488744448 bytes ... done
Writing 693895880 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_16 ; empty space on disk = 557703374045184 bytes ...Writing 711778936 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_4 ; empty space on disk = 557703374045184 bytes ... done
done
Writing 716647096 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_17 ; empty space on disk = 557901747847168 bytes ... done
Writing 607630608 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_11 ; empty space on disk = 557901747847168 bytes ... done
Writing 617221088 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_1 ; empty space on disk = 557866515693568 bytes ... done
Writing 691484720 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_8 ; empty space on disk = 557790414241792 bytes ... done
Writing 676514824 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_12 ; empty space on disk = 557790414241792 bytes ... done
Writing 695820496 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_3 ; empty space on disk = 557790414241792 bytes ... done
Writing 473014568 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_21 ; empty space on disk = 558566701268992 bytes ... done
Writing 698072512 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_20 ; empty space on disk = 558566701268992 bytes ... done
Writing 425945584 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_35 ; empty space on disk = 558464543752192 bytes ... done
Writing 636994472 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_28 ; empty space on disk = 558452329938944 bytes ... done
Writing 666086160 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_29 ; empty space on disk = 558452329938944 bytes ... done
Writing 671041168 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_26 ; empty space on disk = 558842970636288 bytes ... done
Writing 655436280 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_25 ; empty space on disk = 558803510624256 bytes ... done
Writing 678678896 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_34 ; empty space on disk = 558850889482240 bytes ... done
Writing 656936960 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_27 ; empty space on disk = 558850889482240 bytes ... done
Writing 688728680 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_23 ; empty space on disk = 558790776717312 bytes ... done
Writing 705631336 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_38 ; empty space on disk = 558790776717312 bytes ... done
Writing 722617208 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_30 ; empty space on disk = 559032637063168 bytes ...Writing 696546608 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_32 ; empty space on disk = 559032637063168 bytes ... done
done
Writing 588203560 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_37 ; empty space on disk = 559007605456896 bytes ... done
Writing 700730480 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_22 ; empty space on disk = 558951636664320 bytes ... done
Writing 682579136 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_39 ; empty space on disk = 558951636664320 bytes ... done
Writing 714028824 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_33 ; empty space on disk = 558951636664320 bytes ... done
Writing 661184600 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_31 ; empty space on disk = 558931638222848 bytes ... done
Writing 708459240 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_24 ; empty space on disk = 558929423630336 bytes ... done
Writing 705286808 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_36 ; empty space on disk = 558988628328448 bytes ... done
Writing 686529600 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_41 ; empty space on disk = 559062246752256 bytes ... done
Writing 658735520 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_40 ; empty space on disk = 559029900279808 bytes ... done
Writing 532708784 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_43 ; empty space on disk = 559273872457728 bytes ... done
Writing 552891144 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_45 ; empty space on disk = 559273872457728 bytes ...Writing 602156544 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_42 ; empty space on disk = 559273872457728 bytes ... done
done
Writing 539997440 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_55 ; empty space on disk = 559258303201280 bytes ... done
Writing 721584104 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_46 ; empty space on disk = 559248706633728 bytes ... done
Writing 628882096 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_52 ; empty space on disk = 559248706633728 bytes ... done
Writing 581274728 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_54 ; empty space on disk = 559244344557568 bytes ... done
Writing 628226392 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_53 ; empty space on disk = 559234546663424 bytes ... done
Writing 691722736 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_51 ; empty space on disk = 559234546663424 bytes ... done
Writing 678301216 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_47 ; empty space on disk = 559226225164288 bytes ... done
Writing 725820112 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_48 ; empty space on disk = 559413233451008 bytes ... done
Writing 562829872 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_58 ; empty space on disk = 559408334503936 bytes ... done
Writing 729973184 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_44 ; empty space on disk = 559408334503936 bytes ...Writing 710575720 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_49 ; empty space on disk = 559408334503936 bytes ... done
done
Writing 534651664 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_59 ; empty space on disk = 559408334503936 bytes ... done
Writing 624651016 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_61 ; empty space on disk = 559456988430336 bytes ... done
Writing 713298920 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_57 ; empty space on disk = 559456988430336 bytes ... done
Writing 695824568 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_50 ; empty space on disk = 559382698917888 bytes ... done
Writing 683654488 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_56 ; empty space on disk = 559649456652288 bytes ... done
Writing 622990080 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_60 ; empty space on disk = 559631572140032 bytes ... done
Writing 665619472 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_63 ; empty space on disk = 559629827309568 bytes ... done
Writing 678918424 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_62 ; empty space on disk = 559582564843520 bytes ... done
Writing 654838016 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_66 ; empty space on disk = 559628802850816 bytes ... done
Writing 595952760 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_64 ; empty space on disk = 559619608936448 bytes ... done
Writing 614194176 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_67 ; empty space on disk = 559610884784128 bytes ... done
Writing 556574392 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_65 ; empty space on disk = 559918400667648 bytes ... done
Writing 646278680 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_70 ; empty space on disk = 559960343707648 bytes ... done
Writing 635442848 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_69 ; empty space on disk = 559962289864704 bytes ... done
Writing 725545584 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_72 ; empty space on disk = 559961081905152 bytes ... done
Writing 644117496 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_68 ; empty space on disk = 559961618776064 bytes ... done
Writing 707023008 bytes into /n/scratch3/users/w/wn19/hg38_index//SA_71 ; empty space on disk = 559716982849536 bytes ... done
Mar 11 14:52:37 ... loading chunks from disk, packing SA...
Mar 11 14:54:19 ... finished generating suffix array
Mar 11 14:54:19 ... generating Suffix Array index
Mar 11 14:57:48 ... completed Suffix Array index
Mar 11 14:57:49 Finished preparing junctions
Mar 11 14:57:49 ..... inserting junctions into the genome indices
Mar 11 14:58:18 Finished SA search: number of new junctions=394973, old junctions=0
Mar 11 14:59:05 Finished sorting SA indicesL nInd=156407526
Genome size with junctions=3216987595 3138387968 78599627
GstrandBit1=32 GstrandBit=32
Mar 11 15:00:31 Finished inserting junction indices
Mar 11 15:00:59 Finished SAi
Mar 11 15:00:59 ..... finished inserting junctions into genome
Mar 11 15:00:59 ... writing Genome to disk ...
Writing 3216987595 bytes into /n/scratch3/users/w/wn19/hg38_index//Genome ; empty space on disk = 559516676521984 bytes ... done
SA size in bytes: 24948435851
Mar 11 15:01:05 ... writing Suffix Array to disk ...
Writing 24948435851 bytes into /n/scratch3/users/w/wn19/hg38_index//SA ; empty space on disk = 559509026111488 bytes ... done
Mar 11 15:01:53 ... writing SAindex to disk
Writing 8 bytes into /n/scratch3/users/w/wn19/hg38_index//SAindex ; empty space on disk = 559490235629568 bytes ... done
Writing 120 bytes into /n/scratch3/users/w/wn19/hg38_index//SAindex ; empty space on disk = 559490235629568 bytes ... done
Writing 1565873491 bytes into /n/scratch3/users/w/wn19/hg38_index//SAindex ; empty space on disk = 559490235629568 bytes ... done
Mar 11 15:01:58 ..... finished successfully
DONE: Genome generation, EXITING
-----------------------------------
genomeParameters.txt
### STAR --runMode genomeGenerate --runThreadN 20 --genomeDir /n/scratch3/users/w/wn19/hg38_index --genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf --sjdbOverhang 99
### GstrandBit 32
versionGenome 2.7.4a
genomeType Full
genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeTransformType None
genomeTransformVCF -
sjdbOverhang 99
sjdbFileChrStartEnd -
sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbInsertSave Basic
genomeFileSizes 3216987595 24948435851
-----------------------------
On Mar 15, 2022, at 9:42 AM, Alexander Dobin ***@***.***> wrote:
Hi Werner,
please send me the Log.out files for genome indexing and mapping runs.
Thanks!
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The mapping Log.out file is missing these lines at the top: I think you are using a different (older) version of STAR for mapping. I recommend using the full path to the executable to make sure you are using the same one for indexing and mapping. |
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Hi Alex,
that’s strange - I am specifying version 2.7.9a in the script (see below).
2.7.9a is also the default version on the server.
is there a better way to make sure 2.7.9a is used for the indexing?
Many thanks, Werner
#!/bin/bash
#SBATCH -p short # partition name
#SBATCH -t 0-6:00 # hours:minutes runlimit after which job will be killed
#SBATCH -c 20 # number of cores requested -- this needs to be greater than or equal to the number of cores you plan to use to run your job
#SBATCH --mem 64G
#SBATCH --job-name STAR_genome_index # Job name
#SBATCH -o %j.out # File to which standard out will be written
#SBATCH -e %j.err # File to which standard err will be written
module load gcc/6.2.0 star/2.7.9a
# needs genome fasta and gif files in home/wn19/
# index file will be generated in n/scratch3/users/w/wn19/
STAR --runThreadN 20 \
--runMode genomeGenerate \
--genomeDir /n/scratch3/users/w/wn19/hg38_index \
--genomeFastaFiles /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.dna.primary_assembly.fa \
--sjdbGTFfile /home/wn19/reference_data_STAR/Homo_sapiens.GRCh38.105.gtf \
--sjdbOverhang 99
… On Mar 15, 2022, at 10:36 AM, Alexander Dobin ***@***.***> wrote:
The mapping Log.out file is missing these lines at the top:
STAR version=2.7.9a
STAR compilation time,server,dir=2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
I think you are using a different (older) version of STAR for mapping. I recommend using the full path to the executable to make sure you are using the same one for indexing and mapping.
—
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I think the module loading command did not work. |
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yes, I have STAR 2.7.10a on my computer but I never got the indexing to work there even with the pre-compiled version.
so I ran the indexing and alignment on the server.
… On Mar 15, 2022, at 11:45 AM, Alexander Dobin ***@***.***> wrote:
I think the module loading command did not work.
How did you run the indexing step? Did you have STAR executable somewhere else?
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The easiest way to ensure you are using a certain version of STAR is to use the STAR executable |
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great, many thanks. this seems to have solved the issue!
all the best, Werner
… On Mar 16, 2022, at 11:38 AM, Alexander Dobin ***@***.***> wrote:
The easiest way to ensure you are using a certain version of STAR is to use the STAR executable
STAR-2.7.9a/bin/Linux_x86_64_static/STAR to the server, and then call it with the full path.
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Hi,
I am getting an error message when trying to compile STAR 2.7.10a on my mac using gcc/11.2.0_3/bin/g++-11:
direct access in function '__ZnamRKSt9nothrow_t.cold' from file '/usr/local/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/x86_64-apple-darwin21/11/../../../libstdc++.a(new_opvnt.o)' to global weak symbol '__ZnamRKSt9nothrow_t' from file '/usr/local/Cellar/gcc/11.2.0_3/bin/../lib/gcc/11/gcc/x86_64-apple-darwin21/11/../../../libstdc++.a(new_opvnt.o)' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
here is what I did:
$wget https://github.com/alexdobin/STAR/archive/2.7.10a.tar.gz
$tar -xzf 2.7.10a.tar.gz
$cd STAR-2.7.10a/source
$make STARforMacStatic CXX=/usr/local/Cellar/gcc/11.2.0_3/bin/g++-11
would you have any advice how to resolve this?
many thanks, Werner
STAR compilation error.txt
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