Does ONCOCNV work with probe base library designated BAM files #16
Description
Dear authors,
at first I thanks for your very use-full software specially in amplicon based targeted panel that compatible with FISH results.
I try to analysis data of targeted panel that designed based on probe base library preparation.
BED file is like the following line
chr1 46714067 46714090 242431688 RAD54L
but I receive this error
$ sudo sh ONCOCNV.sh
ONCOCNV 7.0 - a package to detect copy number changes in Deep Sequencing data
/home/ngs/data/BAMfiles/HRD contains the following files:
total 14285580
-rwxr-xr-x 1 ngs ngs 5425236953 Jul 27 23:07 4control.bam
-rwxr-xr-x 1 ngs ngs 7069752344 Jul 27 18:19 5control.bam
-rwxr-xr-x 1 ngs ngs 2133428085 Jul 25 15:21 M03-12314.bam
running ONCOCNV_getCounts.pl on control samples
number of targeted regions: 0
--Coordinates are read--
Detected 2 control sample(s)
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
reading 4control.bam
sample name: 4control
read 100000 reads
read 200000 reads
read 300000 reads
read 400000 reads
read 500000 reads
read 600000 reads
read 700000 reads
read 800000 reads
read 900000 reads
read 1000000 reads
read 1100000 reads
read 1200000 reads
read 1300000 reads
read 1400000 reads
read 1500000 reads
read 1600000 reads
read 1700000 reads
read 1800000 reads
read 1900000 reads
read 2000000 reads
read 2100000 reads
read 2200000 reads
read 2300000 reads
read 2400000 reads
read 2500000 reads
read 2600000 reads
read 2700000 reads
read 2800000 reads
read 2900000 reads
read 3000000 reads
read 3100000 reads
read 3200000 reads
read 3300000 reads
read 3400000 reads
read 3500000 reads
[E::bgzf_uncompress] Inflate operation failed: 3
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
samtools view: error reading file "4control.bam"
samtools view: error closing "4control.bam": -1
reading 5control.bam
sample name: 5control
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_uncompress] Inflate operation failed: 3
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
samtools view: error reading file "5control.bam"
samtools view: error closing "5control.bam": -1
Total target length: 0
processed 2 controls, 4control 5control
Total target length: 0
/home/ngs/outputDEEPCNA//Control.stats.txt was created
-rw-r--r-- 1 root root 45 Dec 4 10:20 /home/ngs/outputDEEPCNA//Control.stats.txt
running ONCOCNV_getCounts.pl on tumor samples
--Coordinates are read--
Total target length: 0
Detected 1 tumor sample(s)
reading M03-12314.bam
read 1000000 reads
read 2000000 reads
read 3000000 reads
/home/ngs/outputDEEPCNA//Test.stats.txt was created
-rw-r--r-- 1 root root 27 Dec 4 10:25 /home/ngs/outputDEEPCNA//Test.stats.txt
creating target.bed
-rw-r--r-- 1 root root 0 Dec 4 10:25 /home/ngs/outputDEEPCNA//target.bed
creating target.GC.txt
..Oops.. File /home/ngs/outputDEEPCNA//target.fasta is empty!
..It seems that there is not 'chr' prefixes in your reference genome fasta file..
..But no worries! OncoCNV will adjust for it
-rw-r--r-- 1 root root 10 Dec 4 10:25 /home/ngs/outputDEEPCNA//target.GC.txt
running processControl.R
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Error in if (minFrac < minFractionOfShortOrLongAmplicons & maxFrac < minFractionOfShortOrLongAmplicons) { :
missing value where TRUE/FALSE needed
Execution halted
ls: cannot access '/home/ngs/outputDEEPCNA//Control.stats.Processed.txt': No such file or directory
running processSamples.R
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
PSCBS v0.66.0 (2021-10-23 07:40:02 UTC) successfully loaded. See ?PSCBS for help.
Attaching package: 'PSCBS'
The following objects are masked from 'package:base':
append, load
R.cache v0.16.0 (2022-07-21 16:20:02 UTC) successfully loaded. See ?R.cache for help.
Loading required package: lattice
Loading required package: grid
Loading required package: parallel
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '/home/ngs/outputDEEPCNA//Control.stats.Processed.txt': No such file or directory
Execution halted