Error in postalign_xcor.bds line 98

[am33567]

Hi, I send a job with the command:

bds_scr AvFw_ATAC_mul2 /home/am2622/bin/atac_dnase_pipelines/atac.bds -species Av -nth 14 -fastq1_1 "/home/am2622/ATAC/Av/ATAC034_AvM5thFw1_R1.fastq.gz" -fastq1_2 "/home/am2622/ATAC/Av/ATAC034_AvM5thFw1_R2.fastq.gz" -fastq2_1 "/home/am2622/ATAC/Av/ATAC037_AvM5thFw2_R1.fastq.gz" -fastq2_2 "/home/am2622/ATAC/Av/ATAC037_AvM5thFw2_R2.fastq.gz" -fastq3_1 "/home/am2622/ATAC/Av/ATAC040_AvM5thFw3_R1.fastq.gz" -fastq3_2 "/home/am2622/ATAC/Av/ATAC040_AvM5thFw3_R2.fastq.gz" -enable_idr -mem_macs2 15G -mem_bwt2 15G -multimapping 2

and the pipeline worked until the xcor step. Here is the log file: AvFw_ATAC_mul2.BDS.log

Thanks,

Anyi

[leepc12]

https://github.com/kundajelab/phantompeakqualtools/issues/3

Can you add -extra_param_xcor '--max-ppsize=500000' to the command line and try again? If that doesn't work you can simply disable cross-corr analysis by adding -no_xcor

[am33567]

I run the pipeline again with the modifications and now says: "Illegal argument --max-ppsize=500000" It is falling at the same point: part of the log after alignment and removal of duplicates.

Task has finished (51 seconds). Task has finished (49 seconds). Task has finished (36 seconds). 01:26:39.030 ExecutionerLocal 'Local[44]': Tasks [Local[44]] Pending: 1 Running: 2 Done: 26 Failed: 0	PID	Task state	Task name	Dependencies	Task definition
	pending (SCHEDULED)	subsample_tag_PE_4_xcor rep3		zcat /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep3/ATAC041_AvM5thHw3_R1.PE2SE.nodup.tn5.tagAlign.gz	sed N;s/ n/ t/ > /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep3/ATAC041_AvM5thHw3_R1.PE2SE.nodup.tn5.joined; cat /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep3/ATAC041_AvM5thHw3_R1.PE2SE.nodup.tn5.j
19198	running (RUNNING)	dedup_bam_PE_2 rep1		samtools view -F 1804 -f 2 -b /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep1/ATAC035_AvM5thHw1_R1.PE2SE.dupmark.bam > /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep1/ATAC035_AvM5thHw1_R1.PE2SE.nodup.bam; sambamba index -t 6 /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep1/ATAC035_AvM5thHw1_R1.PE2SE.nodup.
23932	running (RUNNING)	spr_tag_PE rep2		zcat /local/workdir/Mimi/ATAC/Av/Hw/out/align/rep2/ATAC038_AvM5thHw2_R1.PE2SE.nodup.tn5.tagAlign.gz	sed N;s/ n/ t/ > /local/workdir/Mimi/ATAC/Av/Hw/out/align/pseudo_reps/rep2/pr1/ATAC038_AvM5thHw2_R1.PE2SE.nodup.tn5.joined; nlines=$( cat /local/workdir/Mimi/ATAC/Av/Hw/out/align/pseudo_reps/rep2/

Task has finished (38 seconds). Task has finished (27 seconds). Error in parse.arguments(args) : Illegal argument --max-ppsize=500000 Execution halted Task failed: Program & line : '/home/am2622/bin/atac_dnase_pipelines/modules/postalign_xcor.bds', line 98 Task Name : 'xcor rep3' Task ID : 'atac.bds.20180508_102943_948_parallel_43/task.postalign_xcor.xcor_rep3.line_98.id_52' Task PID : '24306' Task hint : 'if [[ $(which run_spp_nodups.R 2> /dev/null | wc -l || echo) == "1" ]]; then RUN_SPP=$(which run_spp_nodups.R);; else RUN_SPP=$(which run_spp.R);; fi; Rscript ${RUN_SPP} -rf; -c=/local/workdir/Mimi/ATAC/Av/Hw/out/align/rep3/ATAC041_AvM5thHw3_R1.PE2SE.nodup.tn5.no_chrM.25M.R1.tagAlign.gz -p=4; -filtc' Task resources : 'cpus: 4 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/local/workdir/Mimi/ATAC/Av/Hw/out/align/rep3/ATAC041_AvM5thHw3_R1.PE2SE.nodup.tn5.no_chrM.25M.R1.tagAlign.gz]'

[leepc12]

Please post a full log.

[am33567]

AvHw_ATAC_mul2.BDS.log

[leepc12]

Please update your code with git pull and replace -extra_param_xcor '-max-ppsize=500000' with just -max_ppsize_xcor 500000 and try again?

[am33567]

it worked! Thanks.