veg / haplotype-reconstruction Goto Github PK

I'm trying to run the haplotypers on the Silverback cluster on the HIV data and am getting errors when running aBayesQR and regresshaplo (and savage but the problems with that are already known).

When I run aBayesQR, it fails on the last step (running aBayesQR on the aligned reads) and returns the following error:

Error in rule abayesqr:
jobid: 0
output: output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/config, output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/test_Freq.txt, output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/test_Seq.txt, output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/test_ViralSeq.txt, output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/haplotypes.fasta

RuleException:
CalledProcessError in line 519 of /home/nickeener/haplotype-reconstruction/Snakefile:
Command 'set -euo pipefail; aBayesQR output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/config' returned non-zero exit status 127.
File "/home/nickeener/haplotype-reconstruction/Snakefile", line 519, in __rule_abayesqr
File "/home/nickeener/anaconda3/envs/haplotype-reconstruction/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Removing output files of failed job abayesqr since they might be corrupted:
output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/config
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

I used this command to get that result:
snakemake --cluster 'qsub -o ./logs -e ./logs -V -d pwd-l nodes=1:ppn=2' -j 1 -k output/SRR961669-PacBio/fastp/bowtie2/pol/abayesqr/haplotypes.fasta

With regresshaplo, it doesn't even run, giving this error message as soon as I run the command:

MissingRuleException:
No rule to produce output/SRR961669-PacBio/fastp/bowtie2/pol/regresshaplo/haplotypes.fasta (if you use input functions make sure that they don't raise unexpected exceptions).

This was the command that was used:
snakemake --cluster 'qsub -o ./logs -e ./logs -V -d pwd-l nodes=1:ppn=1' -j 1 -k output/SRR961669-PacBio/fastp/bowtie2/pol/regresshaplo/haplotypes.fasta

Am I doing something wrong here or are these actual bugs?