Bug when dropping short read in a pair

[markziemann]

The following error happens when one read of the pair is very short, and is excluded from the analysis. The remaining read should be reassigned but the renaming isn't working.

+ rm ERR1157768_2_fastqc.zip ERR1157768_2_fastqc.html
++ sed -n 2~4p ERR1157768_2.fastq
++ awk '{print length($1)}'
++ sort -g
++ head -1
+ FQ2_MIN_LEN=4
++ sed -n 2~4p ERR1157768_2.fastq
++ awk '{print length($1)}'
++ numaverage -M
+ FQ2_MEDIAN_LEN=4
++ sed -n 2~4p ERR1157768_2.fastq
++ awk '{print length($1)}'
++ sort -gr
++ head -1
+ FQ2_MAX_LEN=4
+ [[ 61 -lt 20 ]]
+ [[ 61 -ge 20 ]]
+ [[ 4 -lt 20 ]]
+ rm ERR1157768_2.fastq
++ echo ERR1157768_1.fastq
++ sed s/_1//
+ FQ1NEW=ERR1157768.fastq
+ mv ERR1157768_1.fastq ERR1157768.fastq
+ FQ1=ERR1157768.fastq
+ RDS=SE
+ [[ 61 -lt 20 ]]
+ echo ERR1157768 if colorspace, then quit
ERR1157768 if colorspace, then quit
+ '[' FALSE == TRUE ']'
+ echo ERR1157768 Dump the fastq file
ERR1157768 Dump the fastq file
+ rm ERR1157768.fastq
+ '[' FALSE == FALSE ']'
++ nproc
+ parallel-fastq-dump --threads 32 --outdir . --split-files --defline-qual + -s ERR1157768.sra
extra args: ['--split-files', '--defline-qual', '+']
spots: 87215
tempdir: /tmp/pfd_1hhcfnh6

du: cannot access 'ERR1157768.fastq': No such file or directory
+ FILESIZE=
+ FILESIZE=0
+ echo ERR1157768 file size 0
+ tee -a ERR1157768.log
ERR1157768 file size 0
+ rm ERR1157768.sra
+ '[' 0 -eq 0 ']'
+ echo ERR1157768 has no reads. Aborting
+ tee -a ERR1157768.attempts.txt
ERR1157768 has no reads. Aborting

[markziemann]

Has been fixed in the latest commit.

o

• '[' PE == PE ']'
• [[ 61 -ge 20 ]]
• [[ 4 -lt 20 ]]
• echo Read 2 is too short. Omitting from downstream analysis.
• tee -a ERR1157770.log Read 2 is too short. Omitting from downstream analysis.
• rm ERR1157770_2.fastq ++ echo ERR1157770_1.fastq ++ sed s/_1//
• FQ1NEW=ERR1157770.fastq
• mv ERR1157770_1.fastq ERR1157770.fastq
• FQ1=ERR1157770.fastq
• RDS=SE
• [[ 61 -lt 20 ]] ++ du -s ERR1157770.fastq ++ cut -f1
• FILESIZE=115944
• FILESIZE=115944
• echo ERR1157770 file size 115944
• tee -a ERR1157770.log ERR1157770 file size 115944
• rm ERR1157770.sra
• '[' 115944 -eq 0 ']'
• echo ERR1157770 completed basic pipeline successfully
• tee -a ERR1157770.log ERR1157770 completed basic pipeline successfully
• echo ERR1157770 Quality trimming ERR1157770 Quality trimming
• '[' SE == SE ']'
• skewer -l 18 -q 10 -k inf -t 32 -o ERR1157770 ERR1157770.fastq

Final metrics look really good

QualityEncoding: Read1MinimumLength:61 Read1MedianLength:61 Read1MaxLength:61 Read2MinimumLength:4 Read2MedianLength:4 Read2MaxLength:4 NumReadsTotal:614206 NumReadsQcPass:360448 QcPassRate:58.6852% PE_Read1_StarMapRateTest:55 PE_Read2_StarMapRateTest:NA PE_Read1_Excluded:FALSE PE_Read2_Excluded:FALSE MappingFormat:SE STAR_UniqMappedReads:332923 STAR_Strandedness:PositiveStrand STAR_UnmappedReads:70056 STAR_MultiMappedReads:202252 STAR_NoFeatureReads:111202 STAR_AmbiguousReads:2689 STAR_AssignedReads:219032 STAR_UniqMapRate:92.3637% STAR_AssignRate:60.7666% Kallisto_MappedReads:82675 Kallisto_MapRate:22.9367%