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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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VFDB cannot be executed from the middle. #124

Closed Iwashita-N closed 3 years ago

Iwashita-N commented 4 years ago

srst2 --input_pe /home/iwashita/work/Iguchi/read/APJ-1_S215_L002_R1_001.fastq /home/iwashita/work/Iguchi/read/APJ-1_S215_L002_R2_001.fastq --output APJ-1 --forward _R1 --reverse _R2 --log --gene_db Escherichia_VF2_clustered.fasta

When you check the log output as a result of execution,

01/16/2020 16:09:51 Reference name is found second time in line @SQ SN:874__gb LN:117

01/16/2020 16:09:59 Processing Bowtie2 output with SAMtools... 01/16/2020 16:09:59 Generate and sort BAM file... 01/16/2020 16:09:59 Running: /home/software/bin/samtools-0.1.18 view -b -o APJ-1APJ-1.Escherichia_VF2_clustered.unsorted.bam -q 1 -S APJ-1APJ-1.Escherichia_VF2_clustered.sam.mod 01/16/2020 16:10:03 Running: /home/software/bin/samtools-0.1.18 sort APJ-1APJ-1.Escherichia_VF2_clustered.unsorted.bam APJ-1APJ-1.Escherichia_VF2_clustered.sorted 01/16/2020 16:10:12 Deleting sam and bam files that are not longer needed... 01/16/2020 16:10:12 Deleting APJ-1APJ-1.Escherichia_VF2_clustered.sam 01/16/2020 16:10:12 Deleting APJ-1APJ-1.Escherichia_VF2_clustered.sam.mod 01/16/2020 16:10:12 Deleting APJ-1APJ-1.Escherichia_VF2_clustered.unsorted.bam 01/16/2020 16:10:12 Generate pileup... 01/16/2020 16:10:12 Running: /home/software/bin/samtools-0.1.18 mpileup -L 1000 -f Escherichia_VF2_clustered.fasta -Q 20 -q 1 -B APJ-1APJ-1.Escherichia_VF2_clustered.sorted.bam 01/16/2020 16:10:14 Processing SAMtools pileup...

It is finished at this point.

There are four output files below, and there is no content for APJ-1genesEscherichia_VF2_clustered__results.txt.

How do you solve it?

There are 203 files that can be executed, and 71 files that cannot be executed as described above.

srst2 0.2.0 bowtie2.2.9 samtools-0.1.18

Professor please.