FAQ

Frequently Asked Questions

1. 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.

2. 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.

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