Failed to solve scheduling problem with ILP solver
Closed this issue · 3 comments
ch8316f5eyu commented
Hi,
when I run mcclintock, this error occured:
PROCESSING making coverage fasta
PROCESSING coverage fasta created
PROCESSING making reference fasta
PROCESSING making consensus fasta
PROCESSING consensus fasta created
PROCESSING prepping reads for McClintock
PROCESSING formatting the name of consensus TE fasta headers for compatibility with relocaTE
PROCESSING relocaTE consensus fasta created
PROCESSING reference fasta created
PROCESSING adding fake chromosomes if chrom # < 5, required by TE-locate
PROCESSING making samtools and bwa index files for reference fasta &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/processing.log
PROCESSING Running RepeatMasker for RelocaTE2 &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/processing.log
PROCESSING TE-locate reference created
PROCESSING creating 2bit file from reference genome fasta &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/processing.log
PROCESSING reference 2bit file created
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
PROCESSING running trim_galore &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/trimgalore.log
[INFO ] multiqc : This is MultiQC v1.9 (043bffd)
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/trimgalore
[INFO ] cutadapt : Found 2 reports
[INFO ] fastqc : Found 2 reports
[INFO ] multiqc : Compressing plot data
[INFO ] multiqc : Report : multiqc_report.html
[INFO ] multiqc : Data : multiqc_data
[INFO ] multiqc : MultiQC complete
PROCESSING read setup complete
NGS_TE_MAPPER2 running ngs_te_mapper2 &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/ngs_te_mapper2.log
PROCESSING samtools and bwa index files for reference fasta created
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
I have no idea what is it and how to solve it.
pbasting commented
Hi @ch8316f5eyu,
The Failed to solve scheduling problem with ILP solver is not a fatal error. It is just a message from snakemake stating that the ILP solver failed and that it will use the greedy solver instead. I have yet to see the greedy solver fail on any of my runs. McClintock should run fine despite this warning message. Try letting the job run to completion even if you see this message. If any other errors occur, let me know.
Thanks,
Preston
ch8316f5eyu commented
Hi @pbasting
This is the new error:
python /home/data/gmb23/app/mcclintock/install/tools/teflon/teflon_prep_annotation.py -wd /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/teflon/unfiltered/ -a /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/teflon/unfiltered/reference_te.bed -t /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/teflon/unfiltered/teflon_taxonomy.tsv -f /home/data/gmb23/project/Primed_Naive_exon/mcclintock/GRCm38.primary_assembly.genome/consensus_fasta/consensusTEs.fasta -g /home/data/gmb23/project/Primed_Naive_exon/mcclintock/GRCm38.primary_assembly.genome/genome_fasta/GRCm38.primary_assembly.genome.fasta -p teflon
[Wed Feb 10 22:39:47 2021]
Error in rule teflon_preprocessing:
jobid: 12
output: /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/teflon/unfiltered/reference_te.bed, /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/teflon/unfiltered/teflon_taxonomy.tsv, /home/data/gmb23/project/Primed_Naive_exon/mcclintock/ESC_Naive_R1/results/teflon/unfiltered/teflon.sorted.bam
conda-env: /home/data/gmb23/app/mcclintock/install/envs/conda/f3368e68
RuleException:
CalledProcessError in line 25 of /home/data/gmb23/app/mcclintock/snakefiles/teflon.snakefile:
Command 'source /home/data/gmb23/miniconda3/envs/mcclintock/bin/activate '/home/data/gmb23/app/mcclintock/install/envs/conda/f3368e68'; set -euo pipefail; /home/data/gmb23/miniconda3/envs/mcclintock/bin/python3.7 /home/data/gmb23/project/Primed_Naive_exon/mcclintock/snakemake/9765619/.snakemake/scripts/tmpvkpxvwjq.teflon_pre.py' returned non-zero exit status 1.
File "/home/data/gmb23/miniconda3/envs/mcclintock/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 2340, in run_wrapper
File "/home/data/gmb23/app/mcclintock/snakefiles/teflon.snakefile", line 25, in __rule_teflon_preprocessing
File "/home/data/gmb23/miniconda3/envs/mcclintock/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 568, in _callback
File "/home/data/gmb23/miniconda3/envs/mcclintock/lib/python3.7/concurrent/futures/thread.py", line 57, in run
File "/home/data/gmb23/miniconda3/envs/mcclintock/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 554, in cached_or_run
File "/home/data/gmb23/miniconda3/envs/mcclintock/lib/python3.7/site-packages/snakemake/executors/__init__.py", line 2352, in run_wrapper
COVERAGE augmenting reference genome
COVERAGE samtools and bwa indexing reference &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/coverage.log
COVERAGE samtools and bwa indexing reference &> /home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/coverage.log
Thank you for your help
pbasting commented
Hi @ch8316f5eyu,
- It looks like something is going wrong with the TEFLoN preprocessing module but I'll need to see the TEFLoN log to try and determine what is happening.
- Can you attach your teflon log to a post on this issue so that I can look through it? Based on the log you posted, it should be at:
/home/data/gmb23/project/Primed_Naive_exon/mcclintock/logs/20210209.165111.9765619/teflon.log
Thanks!
-Preston