1. The exit status of my job wasn't zero! My job won't run! Help!

• The best thing to do for figuring out what went wrong is to look at the error file for the job. This will be located at /your_filepath/sequence_handling/ErrorFiles/PROJECT_HANDLER.eJOBNUMBER where the variables in all caps depend on the job.

2. I got an email from MSI about my job saying "Job exceeded walltime limit" with exit status -11. What happened?

• Jobs can only run for so long on the supercomputer before it kills them. This amount of time is set in the qsub settings for each job, example: "mem=22gb,nodes=1:ppn=4,walltime=6:00:00". If your job ran out of time, try increasing the walltime limit and resubmitting.

• Note that certain queues have maximum walltime limits you can request, as detailed on the MSI queues page. Jobs on lab can only run 24 hours (lab-long is unreliable). For longer jobs, use mesabi.

3. When I run Adapter_Trimming, I only get trimmed singles out even though my data is paired end!

• If you have paired end data, then each sample should have samplename_Forward_ScytheTrimmed.fastq.gz and a samplename_Reverse_ScytheTrimmed.fastq.gz. If you're only getting samplename_Single_ScytheTrimmed.fastq.gz, then you have likely entered FORWARD_NAMING and/or REVERSE_NAMING incorrectly.

4. I'm getting an error when running SAM_Processing using SAMtools. It looks like

[bam_sort_core] merging from 44 files...
[bam_rmdup_core] processing reference morex_contig_1...
[bam_rmdup_core] processing reference morex_contig_4...
/bin/bash: line 1: 26653 Segmentation fault      (core dumped) samtools rmdup "${out}/sorted/${sampleName}_${YMD}_sorted.bam" "${out}/finished/${sampleName}_${YMD}_deduped.bam"
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[E::bam_hdr_read] truncated bam header
Failed to read header for "/home/filepath/SAM_Processing/finished/sample1_deduped.bam"
[bam_sort_core] merging from 50 files...
[bam_rmdup_core] processing reference morex_contig_1...
[bam_rmdup_core] processing reference morex_contig_4...
/bin/bash: line 1: 27530 Segmentation fault      (core dumped) samtools rmdup "${out}/sorted/${sampleName}_${YMD}_sorted.bam" "${out}/finished/${sampleName}_${YMD}_deduped.bam"
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
[E::bam_hdr_read] truncated bam header
Failed to read header for "/home/filepath/SAM_Processing/finished/sample2_deduped.bam"

• The issue here is the version of SAMtools that is being used. Please consult the dependencies page about which version to use.