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jlanga / smsk_trinotate

Snakemake workflow to run transdecoder + trinotate
MIT License
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Error in job trinotate_rnammer while creating output file results/trinotate/rnammer.tsv. #5

Closed mictadlo closed 7 years ago

mictadlo commented 7 years ago

Hi I did snakemake -j 40 --rerun-incomplete --latency-wait 10000 but I got the following Error:

Done.  See output file: assembly.fasta.rnammer.gff

Waiting at most 10000 seconds for missing files.
Error in job trinotate_rnammer while creating output file results/trinotate/rnammer.tsv.
MissingOutputException in line 242 of /scratch/trinotate/smsk_trinotate/src/snakefiles/trinotate.py:
Missing files after 10000 seconds:
results/trinotate/rnammer.tsv
This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.
Finished job 193.

Any idea what I missed?

Thank you in advance.

Michal

jlanga commented 7 years ago

Hi.

Did you modify the Perl scripts that the author of Trinotate recommends?

mictadlo commented 7 years ago

Hi, It seems that the example for rnammer got passed successfully.

(smsk_trinotate) ubuntu@waterhouse-1:/mnt/apps/rnammer/example$ rnammer -S bac -m lsu,ssu,tsu -xml ecoli.xml -gff ecoli.gff -h ecoli.hmmreport < ecoli.fsa
(smsk_trinotate) ubuntu@waterhouse-1:/mnt/apps/rnammer/example$ head ecoli.xml 
<?xml version='1.0'?>
<output>
    <predictionTitle>Prediction of ribosomal RNA</predictionTitle>
    <predictor>RNAmmer-1.2</predictor>
    <reference>Lagesen K, Hallin PF, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes.2007;35(9):3100-8. Epub 2007 Apr 22</reference>
<predictionDate>2017-08-11</predictionDate>
    <entries>
        <entry>
            <mol>5s_rRNA</mol>
            <feature>rRNA</feature>

Any idea what am I missing?

Thank you in advance.

Michal

mictadlo commented 7 years ago

rnammer seems to have genarated files but I still get an error Error in job trinotate_rnammer while creating output file results/trinotate/rnammer.tsv

smsk_trinotate$ ls
assembly27_85_remove0_final.fasta  assembly.fasta.transdecoder_dir  LICENSE    README.md         results    src                         transcriptSuperScaffold.bed
assembly.fasta.rnammer.gff         data                             nohup.out  requirements.txt  Snakefile  tmp.superscaff.rnammer.gff  transcriptSuperScaffold.fasta
smsk_trinotate$ less assembly.fasta.rnammer.gff
comp9579_c0_seq1        RNAmmer rRNA    12      126     72.7    +       .       8s_rRNA
comp76529_c1_seq3       RNAmmer rRNA    851     2660    1513.4  +       .       18s_rRNA
comp76529_c1_seq3       RNAmmer rRNA    2884    6642    3352.1  +       .       28s_rRNA
comp76530_c0_seq1       RNAmmer rRNA    1       528     3352.1  +       .       28s_rRNA
comp76530_c1_seq2       RNAmmer rRNA    1       733     3352.1  +       .       28s_rRNA

Should the above files be moved to results/trinotate/ folder and where the results/trinotate/rnammer.tsv get generated?

Thank you in advance.

Michal

jlanga commented 7 years ago

Hi, I pushed that in a commit in devel.

Anyway, I analyzed the entire Zebrafish transcriptome to end with just one single transcript marked as 18S.