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MeHelmy / princess

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align stage completed successfully but small align bam #5

Closed rozaimirazali closed 3 years ago

rozaimirazali commented 4 years ago

Hello.

I ran the align command

bsub -q normal -e ../logs/align.e -o ../logs/align.o -n 32 "princess align -d ../output/17092020 --ReadType clr -u -e --Aligner minimap --samplesFiles list.txt --ref /gpfs/projects/ymokrab_Lab/REF/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/input/ref/GRCh37.fa --jobs 200 --log align.log"

and it ended succesfully

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 200 Rules claiming more threads will be scaled down. Job counts: count jobs 1 indexBam 1 mergeAlign 1 minimap2 3 cat pictures/start.txt

[Thu Sep 17 16:45:25 2020] Job 1: Running minimap2 , sample is: list.txt

        minimap2  -ax map-pb "/gpfs/projects/ymokrab_Lab/REF/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/input/ref/GRCh37.fa"  "/gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/list.txt" -H "--MD" -t "5" | samtools sort -@ 5 - > "/gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/align/minimap/list.txt.bam"

[Thu Sep 17 16:46:30 2020] Finished job 1. 1 of 3 steps (33%) done

[Thu Sep 17 16:46:30 2020] Job 2: Indexing /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/align/minimap/list.txt.bam

samtools index /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/align/minimap/list.txt.bam [Thu Sep 17 16:46:30 2020] Finished job 2. 2 of 3 steps (67%) done

[Thu Sep 17 16:46:30 2020] Job 0: Mergeing data

    samtools merge -@ 5 /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/align/minimap/data.bam /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/align/minimap/list.txt.bam > /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/align/minimap/merge.log 2>&1

[Thu Sep 17 16:46:30 2020] Finished job 0. 3 of 3 steps (100%) done Complete log: /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/.snakemake/log/2020-09-17T164524.510866.snakemake.log mkdir -p /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/snake_log && find . -maxdepth 1 -name 'snakejob.*' -type f -print0 | xargs -0r mv -t /gpfs/projects/ymokrab_Lab/SDR400076/REF005_Long_read_structural_variants/princess/MNDY02/MNDY0201/output/17092020/snake_log && cat pictures/success.txt

but the output bam seems very small. I tried to check the stderr and the log files but did not find anything wrong. Could you please advise ?

-rw-rw---- 1 rmohamadrazali sysbio 1.5K Sep 17 16:46 list.txt.bam -rw-rw---- 1 rmohamadrazali sysbio 0 Sep 17 16:46 list.txt.log -rw-rw---- 1 rmohamadrazali sysbio 688 Sep 17 16:46 list.txt.bam.bai -rw-rw---- 1 rmohamadrazali sysbio 0 Sep 17 16:46 merge.log -rw-rw---- 1 rmohamadrazali sysbio 1.5K Sep 17 16:46 data.bam

MeHelmy commented 3 years ago

Thank you for reaching back,

The -s command in Princess accepts a list of fasta/fastq files (it could be gzipped also), but you supported it with a text file.

Thanks