Hi, My understanding from other posts is that the bowtie2 “Fatal error: Exit code 1 ()” is likely an issue with FASTQ inputs; I have run these paired-end FASTQ files through bowtie2 before without issue, but this time I processed reads with fastp before bowtie2 so I am confident the error has something to do with fastp output. How do I figure out with is wrong with fastp output and how do I correct it?
Thanks,
Justin
Can you send an error report in to us using the “bug” icon on the failed history item? This will help us track down the specific problem.
Hi Nate, I did last night. I’ve copied the info from the confirmation email below. Unfortunately, I’m under time pressure and my disk quota was full so I made the choice to abandon the fastp route, cleared my disk space deleting the inputs from this job (I’ve left the failed job logs though), and am in the process of reloading the data now to go straight into bowtie2 without preprocessing. Does fastp output generally work as input for bowtie2? I know I’ve made it harder for you to help by deleting the fastp data, but I wasn’t sure when/if I’d get a response. Thanks for any insights you can offer.
Justin
Galaxy Tool Error Report
Error Localization
| Dataset | 44215977 (bbd44e69cb8906b5a210fd6557c6d72b) |
|---|---|
| History | 2917310 (387a03a1eca44028) |
| Failed Job | 2320: Bowtie2 on data 2240 and data 2239: alignments (bbd44e69cb8906b5712e07adcbf51859) |
User Provided Information
The user ‘craigj2@mymail.vcu.edu’ provided the following information:
My understanding is that the “Fatal error: Exit code 1 ()” is likely an issue with FASTQ inputs; I have run these FASTQ files through bowtie2 before without issue, but this time I processed reads with fastp before bowtie2 so I am confident the error has something to do with fastp output. How do I figure out with is wrong with fastp output and how do I correct it? Thanks, Justin
Detailed Job Information
Job environment and execution information is available at the job info page.
| Job ID | 30079910 (bbd44e69cb8906b5cf9cf002ecc44c77) |
|---|---|
| Tool ID | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
| Tool Version | 2.3.4.3+galaxy0 |
| Job PID or DRM id | 24727836 |
| Job Tool Version | /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-5bee08a20f60a5597c4ecd54735d608dc6a44caf6f433cd52f23c80aa5a38d02/bin/bowtie2-align-s version 2.3.4.1 64-bit Built on default-df05fd51-3d07-4109-abba-6883676f3ae8 Mon Jun 25 23:07:08 UTC 2018 Compiler: gcc version 4.8.2 20140120 (Red Hat 4.8.2-15) (GCC) Options: -O3 -m64 -msse2 -funroll-loops -g3 -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -std=c++98 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} |
Job Execution and Failure Information
Command Line
set -o | grep -q pipefail && set -o pipefail; ln -s ‘/galaxy-repl/main/files/044/211/dataset_44211834.dat’ input_f.fastq.gz && ln -s ‘/galaxy-repl/main/files/044/211/dataset_44211835.dat’ input_r.fastq.gz && bowtie2 -p {GALAXY_SLOTS:-4} -x '/galaxy/data/hg38/hg38female/bowtie2_index/hg38female' -1 'input_f.fastq.gz' -2 'input_r.fastq.gz' -I 0 -X 1000 --fr --dovetail --rg-id "INPUT_30_S18_L001_001.fastq" --skip 0 --qupto 3000000000 --trim5 0 --trim3 0 --phred33 -N 1 -L 11 -i 'S,1,1.15' --n-ceil 'L,8,0' --dpad 15 --gbar 1 --no-1mm-upfront --end-to-end --score-min 'L,-0.6,-0.6' --mp '6,2' --np 1 --rdg 5,3 --rfg 5,3 --seed 0 2> '/galaxy-repl/main/files/044/215/dataset_44215978.dat' | samtools sort -@{GALAXY_SLOTS:-2} -O bam -o ‘/galaxy-repl/main/files/044/215/dataset_44215977.dat’
stderr
stdout
Job Information
None
Job Traceback
None
Thanks for pasting your error report, for some reason I haven’t received it via email. I checked the job and it’s very odd, there’s no output from Galaxy’s job scripts or the tool at all, and it only ran on the cluster for 6 seconds. It’s too late now but if the same thing happens again in the future, please give the job another try and report the error.
Regarding fastp -> bowtie2, I don’t know as I’m not familiar with the science side of things, but someone else will hopefully provide some insight on that.
OK, thank you. I will rerun fastp and bowtie2 on new runs/output if you are willing to take another look if/when the error arises again. I did retry the bowtie2 job several times with the same input and another fastp processed dataset and got the same error all times (these inputs also deleted now). I will post a bug report and also reply again here later today when I’ve reproduced the problem. Thanks, Justin
1 Like
The reprocessed job is currently running, and it finished successfully on at least one set of paired-end reads. I’m not sure what has changed but I’m very glad fastp->bowtie2 appears to be working at the moment. Thank you.