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EichlerLab / smrtsv2

Structural variant caller
MIT License
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Error in rule detect_stops_count_per_bin #27

Closed lamevan closed 5 years ago

lamevan commented 5 years ago

Hi,I run the following command...and the reference genome use UCSC name.

smrtsv --tempdir /home/lamevan/temp --jobs 4 run --batches 20 --threads 8 all.chrs.con input.fofn

Could you please explain why I am getting error here?

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 4 Rules claiming more threads will be scaled down.

[Deleted by paudano - moved to attachment]

detect_run_output.txt

[Sun Apr 7 22:27:15 2019] rule detect_stops_count_per_bin: input: detect/stops/hardstops/hardstop_breakpoints.bed, detect/stops/hardstop_bins.bed output: detect/stops/hardstops/hardstop_breakpoints_binned.bed jobid: 32

Error: Invalid record in file detect/stops/hardstops/hardstop_breakpoints.bed. Record is Chr2 -1 0 m150315_201009_42208_c100768742550000001823166207301516_s1_p0/72453/19969_40060 19500 right [Sun Apr 7 22:27:16 2019] Error in rule detect_stops_count_per_bin: jobid: 32 output: detect/stops/hardstops/hardstop_breakpoints_binned.bed

RuleException: CalledProcessError in line 300 of /home/linpeifan/smrtsv2/smrtsv2-master/rules/detect.snakefile: Command ' set -euo pipefail; bedtools intersect -a detect/stops/hardstop_bins.bed -b detect/stops/hardstops/hardstop_breakpoints.bed -sorted -c >detect/stops/hardstops/hardstop_breakpoints_binned.bed ' returned non-zero exit status 1. File "/home/linpeifan/smrtsv2/smrtsv2-master/rules/detect.snakefile", line 300, in __rule_detect_stops_count_per_bin File "/home/linpeifan/smrtsv2/smrtsv2-master/dep/conda/build/envs/python3/lib/python3.6/concurrent/futures/thread.py", line 55, in run Removing output files of failed job detect_stops_count_per_bin since they might be corrupted: detect/stops/hardstops/hardstop_breakpoints_binned.bed [Sun Apr 7 22:28:41 2019] Finished job 31.

Hi,I run the following command...and the reference genome use UCSC name. smrtsv --tempdir /home/lamevan/temp --jobs 4 run --batches 20 --threads 8 all.chrs.con input.fofn

Could you please explain why I am getting error here?

lamevan commented 5 years ago

Maybe the problem occur from that i put 5 bax.h5 file into a bam file..

paudano commented 5 years ago

The error is pretty clear: Error: Invalid record in file detect/stops/hardstops/hardstop_breakpoints.bed. Record is Chr2 -1 0 m150315_201009_42208_c100768742550000001823166207301516_s1_p0/72453/19969_40060 19500 right

Can you attach detect/stops/hardstops/hardstop.bed and detect/stops/hardstops/hardstop_breakpoints.bed? Just drag-and-drop them to the reply, and github will add them as an attachment.

Are the files in input.fofn ".bam" or ".bax.h5" files? We have been seeing some problems running from BAX, but I have not seen this error yet.

lamevan commented 5 years ago

I remove the error line in bed file.it works. thank you!

paudano commented 5 years ago

Ok, it would have been good to see what was causing the bug, but I'm glad it's working.