I'm running the following command -
smrtsv --tempdir ${TMP} --verbose run --runjobs 1,25,50,10 --batches 1 --threads 80 --species Elegans \
--asm-polish arrow --min-support 10 --min-hardstop-support 3 \
${reference} ${inputs}
And I'm getting an error during assembly that I haven't gotten before. I'm using a much larger input file (91X genomewide), so it could be caused because of resource constraints. On a coupe of my runs, the same script, on a fresh run in a new Working directory, ran without any errors, so this is not exactly deterministic either (leading me to believe it could do with computational constraints on Canu)
My error seemed similar to #31 , but when I checked their contig.log v/s mine, I found mine was a different error.
This is my assemble/group/gr-V-9000000-1000000/contig_group.log
Assembly error: Return code = 1
ESC[32m[Sat Nov 9 11:14:22 2019]ESC[0m
ESC[31mError in rule assemble_reads:ESC[0m
ESC[31m jobid: 0ESC[0m
ESC[31m output: region/V-9714696-20875/asm/contigs.fasta, region/V-9714696-20875/asm/contigs.fasta.fai, region/V-9714696-20875/asm/corrected_reads.fastq.gzESC[0m
ESC[31m log: /ufrc/baer/s.ayush/SV_MA/Analysis/smrtsv2/N2.trial2/Strategy2/WS270/Working_directory/assemble/group/gr-V-9000000-1000000/log/V-9714696-20875.logESC[0m
ESC[31mESC[0m
ESC[31mRuleException:
BrokenPipeError in line 370 of /apps/smrtsv/2.0.0/smrtsv2/rules/assemble_group.snakefile:
[Errno 108] Cannot send after transport endpoint shutdown: 'region/V-9714696-20875/asm/contigs.fasta'
File "/apps/smrtsv/2.0.0/smrtsv2/rules/assemble_group.snakefile", line 370, in __rule_assemble_reads
File "/apps/smrtsv/2.0.0/smrtsv2/dep/conda/build/envs/python3/lib/python3.6/concurrent/futures/thread.py", line 55, in runESC[0m
ESC[31mExiting because a job execution failed. Look above for error messageESC[0m
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /ufrc/baer/s.ayush/SV_MA/Analysis/smrtsv2/N2.trial2/Strategy2/WS270/TEMPDIR/asm_group_gr-V-9000000-1000000/.snakemake/log/2019-11-08T054733.501998.snakemake.log
I'm also getting another error (2) in my log files (main log file) -
slurmstepd: error: _is_a_lwp: open() /proc/4793/status failed: No such file or directory
slurmstepd: error: _is_a_lwp: open() /proc/549/status failed: No such file or directory
slurmstepd: error: _is_a_lwp: open() /proc/1843/status failed: No such file or directory
I'm attaching the entire log file. The script is still running despite these errors (if that's relevant). I'm also attaching the contig.log which gave me the error (1)
smrtsv2_N2_trial2.st2.43775083.logcontig_group.log
I'm running the following command - smrtsv --tempdir ${TMP} --verbose run --runjobs 1,25,50,10 --batches 1 --threads 80 --species Elegans \ --asm-polish arrow --min-support 10 --min-hardstop-support 3 \ ${reference} ${inputs}
And I'm getting an error during assembly that I haven't gotten before. I'm using a much larger input file (91X genomewide), so it could be caused because of resource constraints. On a coupe of my runs, the same script, on a fresh run in a new Working directory, ran without any errors, so this is not exactly deterministic either (leading me to believe it could do with computational constraints on Canu)
My error seemed similar to #31 , but when I checked their contig.log v/s mine, I found mine was a different error.
This is my assemble/group/gr-V-9000000-1000000/contig_group.log Assembly error: Return code = 1 ESC[32m[Sat Nov 9 11:14:22 2019]ESC[0m ESC[31mError in rule assemble_reads:ESC[0m ESC[31m jobid: 0ESC[0m ESC[31m output: region/V-9714696-20875/asm/contigs.fasta, region/V-9714696-20875/asm/contigs.fasta.fai, region/V-9714696-20875/asm/corrected_reads.fastq.gzESC[0m ESC[31m log: /ufrc/baer/s.ayush/SV_MA/Analysis/smrtsv2/N2.trial2/Strategy2/WS270/Working_directory/assemble/group/gr-V-9000000-1000000/log/V-9714696-20875.logESC[0m ESC[31mESC[0m ESC[31mRuleException: BrokenPipeError in line 370 of /apps/smrtsv/2.0.0/smrtsv2/rules/assemble_group.snakefile: [Errno 108] Cannot send after transport endpoint shutdown: 'region/V-9714696-20875/asm/contigs.fasta' File "/apps/smrtsv/2.0.0/smrtsv2/rules/assemble_group.snakefile", line 370, in __rule_assemble_reads File "/apps/smrtsv/2.0.0/smrtsv2/dep/conda/build/envs/python3/lib/python3.6/concurrent/futures/thread.py", line 55, in runESC[0m ESC[31mExiting because a job execution failed. Look above for error messageESC[0m Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /ufrc/baer/s.ayush/SV_MA/Analysis/smrtsv2/N2.trial2/Strategy2/WS270/TEMPDIR/asm_group_gr-V-9000000-1000000/.snakemake/log/2019-11-08T054733.501998.snakemake.log
I'm also getting another error (2) in my log files (main log file) - slurmstepd: error: _is_a_lwp: open() /proc/4793/status failed: No such file or directory slurmstepd: error: _is_a_lwp: open() /proc/549/status failed: No such file or directory slurmstepd: error: _is_a_lwp: open() /proc/1843/status failed: No such file or directory
I'm attaching the entire log file. The script is still running despite these errors (if that's relevant). I'm also attaching the contig.log which gave me the error (1) smrtsv2_N2_trial2.st2.43775083.log contig_group.log