Read name provided with no suffix in trimgalore.log

[dgodin19]

Hi,

I get an error in the trimgalore.log that seems to terminate the program, making it so that there is no result output.

The error is:

Read name provided with no suffix
^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H1900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H2900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H3900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H4900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H5900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H6900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H7900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8000000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8100000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8200000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8300000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8400000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8500000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8600000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8700000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8800000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H8900000^H^H^H^H^H^H^H^H^H^H^H^H^H^H^H9000000Scanning complete.

Reads processed: 9032136
Memory used in indexing: ~899 MB

The mcclintock request is:

#!/bin/bash
#$ -N w228
#$ -pe serial 5
#$ -l mfree=8778M
#$ -l h_rt=10:0:0
#$ -wd <wd>
source activate mcclintock
python3 /net/home/mcclintock/mcclintock.py -r /net/home/mcclintock/sacCer2.fasta -c /net/home/mcclintock/test/sac_cer_TE_seqs.fasta -g /net/home/mcclintock/test/reference_TE_locations.gff -t /net/home/mcclintock/test/sac_cer_te_families.tsv -1 /net/home/mcclintock/trimmed/read1.fastq.gz -2 /net/home/mcclintock/trimmed/read2.fastq.gz -o /net/home/mcclintock/w228

What is an example suffix supposed to look like? Does mcclintock work with trimmed reads? If the reads are already trimmed, is there a way to turn off trimgalore?

[cbergman]

Hi @dgodin19

Thanks for your issue report. To help us respond, could you tell me if you were able to successfully get the test dataset to run on your system?

Also, it appears that you are supplying pre-trimmed reads as input. Could you clarify if you are supplying raw or trimmed reads to McClintock.

It is not necessary to supply trimmed reads since McClintock can trim reads for you as part of the run using by default (as you are doing) or by using the -m trimgalore option. If you are supplying trimmed reads as input and then also activating the trimgalore option, it is possible that you might be corrupting your reads in some way. Alternatively, if you are supplying trimmed reads as input, they may have been corrupted prior to being used by McClintock. It is possible that this thread has some leads: https://help.galaxyproject.org/t/trimmomatic-error-fatal-error/9038/5

Thanks,
Casey

[dgodin19]

Hi @cbergman

I am supplying pre trimmed reads as input, and I was wondering if there was a way to run mcclintock without using the trimgalore method.

I will take a look at the resource you provided.

Thank you.

[cbergman]

Hi @dgodin19

Yes, it is possible to run McClintock without using the trimgalore method. By default, McClintock will run all component methods on reads trimmed by trimgalore. However, if you specify the -m option plus a list of component methods, you can allow components to run on your input reads (with no trimming done by trimgalore), e.g.

python3 mcclintock.py \
    -r test/sacCer2.fasta \
    -c test/sac_cer_TE_seqs.fasta \
    -g test/reference_TE_locations.gff \
    -t test/sac_cer_te_families.tsv \
    -1 test/SRR800842_1.fastq.gz \
    -2 test/SRR800842_2.fastq.gz \
    -p 4 \
    -m temp,ngs_te_mapper,retroseq \ #add other methods here
    -o /path/to/output/directory

Please see the readme for more information: https://github.com/bergmanlab/mcclintock/#running-mcclintock-with-specific-component-methods

Hope this helps,
Casey

[cbergman]

Hi @dgodin19

Were you able to run only specific component methods in McClintock by providing pre-trimmed reads as input, as suggested in #104 (comment)? If so, did it solve your original problem with the corrupted read(s)?

Based on a few other bug reports online, I believe your problem is related to fastQC not liking the format of some of the reads in your dataset. See https://help.galaxyproject.org/t/fastq-unavailable-tool-does-not-recognize-inputs-how-to-check-why/8925 & https://help.galaxyproject.org/t/trimmomatic-error-fatal-error/9038.

Perhaps you can try running your untrimmed and trimmed datasets through fastQC directly to determine if your input files have any issues.

Best regards,
Casey

[cbergman]

Hi @dgodin19

Could you confirm if your problem was resolved by following the steps suggested in #104 (comment)? Otherwise, we'll assume it is solved and close at the end of the month.

Best regards,
Casey