(partition_bam_reads) Error: line number 29869383 of file - has 3 fields, but 6 were expected.

[byee4]

Hitting an error in partition_bam_reads:

rule partition_bam_reads:
    input: inputs/star_2_7_gencode40_sjdb/chrNameLength.txt, output/bams/dedup/genome/IP.genome.Aligned.sort.dedup.bam, annotations/gencode.v38.annotation.tiled_partition.bed.gz
    output: output/counts/genome/vectors/IP.counts
    jobid: 0
    benchmark: benchmarks/counts/unassigned_experiment.IP.partition_bam_reads.txt
    reason: Forced execution
    wildcards: replicate_label=IP
    resources: mem_mb=6599, disk_mb=6599, tmpdir=/scratch/bay001/30691944.tscc-mgr7.local

bedtools bamtobed -i output/bams/dedup/genome/IP.genome.Aligned.sort.dedup.bam | awk '($1 != "chrEBV") && ($4 !~ "/2$")' | bedtools flank -s -l 1 -r 0 -g inputs/star_2_7_gencode40_sjdb/chrNameLength.txt -i - | bedtools shift -p 1 -m -1 -g inputs/star_2_7_gencode40_sjdb/chrNameLength.txt -i - | bedtools sort -i - | bedtools coverage -counts -s -a annotations/gencode.v38.annotation.tiled_partition.bed.gz -b - | cut -f 7 | awk 'BEGIN {print "IP"} {print}' > output/counts/genome/vectors/IP.counts;
Error: line number 29869383 of file - has 3 fields, but 6 were expected.
[Fri Feb  3 17:24:31 2023]

[byee4]

Weirdly, running the command on its own completes, so I'm unsure what's going on with the job. Any idea?

[augustboyle]

I've had exactly the same thing happen. I think it happened twice in a row. I tried to troubleshoot but when I ran it manually it completed without error, so I don't know what the issue is.

[byee4]

This kind of error happened again in 'quantify_repeats'

rule quantify_repeats:
    input: /projects/ps-yeolab4/software/eclip/0.7.1/examples/inputs/star_2_7_gencode40_sjdb/chrNameLength.txt, output/bams/dedup/genome/Q0542b_CB_IP_2.genome.Aligned.sort.dedup.bam, /projects/ps-yeolab3/eboyle/encode/pipeline/05_20220720/repeatmasker.grch38.sort.unique.bed.gz
    output: output/counts/repeats/vectors/Q0542b_CB_IP_2.counts
    jobid: 0
    benchmark: benchmarks/repeats/unassigned_experiment.Q0542b_CB_IP_2.quantify_repeats.txt
    reason: Forced execution
    wildcards: replicate_label=Q0542b_CB_IP_2
    resources: mem_mb=6968, disk_mb=6968, tmpdir=/scratch/bay001/32267447.tscc-mgr7.local

bedtools bamtobed -i output/bams/dedup/genome/Q0542b_CB_IP_2.genome.Aligned.sort.dedup.bam | awk '($1 != "chrEBV") && ($4 !~ "/2$")' | bedtools flank -s -l 1 -r 0 -g star_2_7_gencode40_sjdb/chrNameLength.txt -i - | bedtools shift -p 1 -m -1 -g star_2_7_gencode40_sjdb/chrNameLength.txt -i - | bedtools sort -i - | bedtools coverage -s -counts -a repeatmasker.grch38.sort.unique.bed.gz -b - | awk 'BEGIN {print "Q0542b_CB_IP_2"} {print $NF}' > output/counts/repeats/vectors/Q0542b_CB_IP_2.counts
Error: line number 55529334 of file - has 4 fields, but 6 were expected.

Like before, running the command outside of Snakemake finished without error.