empty genes.tsv produced by select_sites.py in rule combined_select_sites

[jazberna1]

Hello,

I am trying to run the pipeline and I have encountered the following.
The rule combined_select_sites produces and empty genes.tsv file.
I see the input arrow files in the workspace/internal_files/group_sites are not empty though.
I am wondering if you would have an idea why select_sites.py produces an empty genes.tsv file. I am testing the pipeline with a small set of reads. Could that be the reason?

Thanks
Jorge

[y9c]

It might because the data do not show sufficient sequencing coverage. Would you please also show me the data under group_sites?

[jazberna1]

Hi @y9c ,

It was possibly due to lack of coverage as I only passed 100 reads so I decided to try with my full fastq files. Then I got an error in the hisat2_3n_mapping_genes_PE rule:

localrule hisat2_3n_mapping_genes_PE:
    input: .tmp/unmapped_internal_PE/CIC_4-rep1_run1_R1.contamination.fq.gz, .tmp/unmapped_internal_PE/CIC_4-rep1_run1_R2.contamination.fq.gz
    output: .tmp/mapping_unsorted_PE/CIC_4-rep1_run1.genes.bam, .tmp/mapping_discarded_PE/CIC_4-rep1_run1.genes.bam, report_reads/mapping/CIC_4-rep1_run1.genes.summary
    jobid: 21
    reason: Forced execution
    wildcards: sample=CIC_4-rep1, rn=run1
    threads: 24
    resources: tmpdir=/scratch/1154727
Select jobs to execute...
(ERR): hisat2-align died with signal 9 (KILL) 
[E::sam_parse1] SEQ and QUAL are of different length

However I checked the files:

.tmp/unmapped_internal_PE/CIC_4-rep1_run1_R1.contamination.fq.gz
.tmp/unmapped_internal_PE/CIC_4-rep1_run1_R2.contamination.fq.gz

and there are no cases where in an particular read the sequence and the quality lines differ in size. There are reads of different lengths due to the adapter trimming I suppose.

is there anything you could think that produces the error when the output of hisat2 goes into samtools?

Thanks
Jorge

[y9c]

Hi @jazberna1, the log you pasted here indicated that the ".tmp/unmapped_internal_PE/CIC_4-rep1_run1_R1.contamination.fq.gz" or ".tmp/unmapped_internal_PE/CIC_4-rep1_run1_R2.contamination.fq.gz" file is truncated, this is most likely due to the error in a previous run. So, it would be better if you can remove these two files, or completely remove the workspace folder, and start the job again.