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jlanga / smsk_trinotate

Snakemake workflow to run transdecoder + trinotate
MIT License
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Unable to set utime on symlink results/raw/assembly.fasta. Your Python build does not support it. #2

Closed mictadlo closed 6 years ago

mictadlo commented 7 years ago

Hi, I got the following error:

rule raw_link_assembly:
    input: assembly27_85_remove0_final.fasta
    output: results/raw/assembly.fasta
    jobid: 61

touch: setting times of 'results/raw/assembly.fasta': Function not implemented
Unable to set utime on symlink results/raw/assembly.fasta. Your Python build does not support it.
Finished job 61.
1 of 280 steps (0.36%) done

What did I miss?

Thak you in advance.

Best wishes,

Michal

mictadlo commented 7 years ago

P.S. After the above problem I got this one:


rule raw_gene_to_trans_map:
    input: results/raw/assembly.fasta
    output: results/raw/gene_to_trans_map.tsv
    log: results/raw/gene_to_trans_map.log
    jobid: 13
    benchmark: results/raw/gene_to_trans_map.json

Error in job trinotate_rnammer while creating output file results/trinotate/rnammer.tsv.
RuleException:
CalledProcessError in line 262 of /scratch/trinotate/smsk_trinotate/src/snakefiles/trinotate.py:
Command 'RnammerTranscriptome.pl --transcriptome results/raw/assembly.fasta --path_to_rnammer /mnt/apps/rnammer/rnammer --org_type euk 2> results/trinotate/rnammer.log' returned non-zero exit status 2.
  File "/scratch/trinotate/smsk_trinotate/src/snakefiles/trinotate.py", line 262, in __rule_trinotate_rnammer
  File "/mnt/apps/miniconda2/envs/smsk_trinotate/lib/python3.6/concurrent/futures/thread.py", line 55, in run
mictadlo commented 7 years ago

The solution for RnammerTranscriptome.pl problem I posted here https://github.com/bioconda/bioconda-recipes/issues/5424 .

jlanga commented 7 years ago

Hi.

About the first error: was it an error or a warning. The "unable to set utime" message is because of using conda:

https://bitbucket.org/snakemake/snakemake/issues/397/unable-to-set-utime-on-symlink-your-python

jlanga commented 7 years ago

About the second message.

Can you paste the contents of the log to know what happened? It should be located in results/raw/gene_to_trans_map.log.

Thanks

jlanga commented 7 years ago

Did you manage to resolve this?