No output written to output dir with silent error

[kate-crosby]

The align subcommand seems to execute fine, but does not finish, and tail -f of log file stops at exactly the same place (whether it's my own or the example Test_Data provided in the repo).

The log file has output, e.g.

kate_crosby@kc-sandbox-2:~/BAD_Mutations$ tail adh3align.log 
===2016-12-01 17:44:57,617 - Pasta_Align===
DEBUG   Cyanidioschyzon_merolae MSSTQGKVIRCKAAVAWKPGQPLSIEEIEVEPPKAGEVRAKVVATGVCHTDAYTLSGADPEGVFPVILGHEGGAIVESVGEGVTSVKPGDHIIPCYIPECGQCKFCRSTKTNLCSAIRVTQGQGLMPDRTTRYSCNGRSLFHYMGCSCFSQYIVLPEIAVAKIRQDAPLDRVCLLGCGITTGIGAVLNTAKVEQGSTVAVFGLGGVGLSVVQGARIAGASRIIGVDTNESKFPLAKQLGATECINPLKFGEKPIQQVLIDMTDGGPDYTFEAIGNVKTMRAALEASHKGWGVSVIIGVAASGEEISTRPFQLVTGRTWKGTAFGGAKSRTQLPELVDMYMKGVINIDDYVTGTYKLDDINRAFEEMHNGRSIRSIILMDDDA
===2016-12-01 17:44:57,618 - Pasta_Align===
DEBUG   Fvesca_226_v1   MSSTEGKVICCRAAVAWEAGKPLVIEEVEVAPPQANEVRVKILYTSLCHTDVYFWEAKGQNPLFPRIYGHEAGGIVESVGEGVTDLKAGDHVLPVFTGECKECDHCKSEESNMCDLLRINTDRGVMLSDGESRFSIKGKPIYHFVGTSTFSEYTVTHVGCLAKINPKAPLDKVCVLSCGISTGLGATLNVAKPKKGSTVAVFGLGAVGLAAAEGARMAGASRIIGVDLTSNRFEEAKKFGITEFVNPKDHKKPVQEVIAELTNGGVDRSIECTGNIQSIISAFESVHDGWGVAVLVGLPPKDAVFTTHPMNFLNERTLKGTFFGNYKPRTDIPSVVEKYMNKELELDKFITHQLPFSQINKAFDYMLKGEGIRCIITMEE*
===2016-12-01 17:44:57,618 - Pasta_Align===
DEBUG   Acoerulea_322_v3        MASISNTTGQIIRCKAAVAWEAGKPLVIEEVEVAPPQAMEVRVKILFTSLCHTDVYFWEAKGQTPLFPRIFGHEAGGIVESVGSGVTDLKPGDHVLPVFTGECKDCAHCKSEESNMCDLLRINTDRGVMLNDGQSRFSINGKPIYHFVGTSTFSEYTVVHVGCLAKINPAAPLDKVCILSCGISTGLGAALNVAKPKQGSTVAVFGLGAVGLAACEGARIAGAKRIIGVDLNSNRFNEAKNFGVTDFVNPKDHNKPVQEVLAEMTDGGVDRSIECTGSVAAMISAFECVHDGWGVAVLVGVPNKDDAFKTHPMNLLNERTLKGTFFGNYKPRSDIPSVVEKYMNKELELEKFITHEVPFSEINKAFEYMLQGKSIRCIIRMEA*
===2016-12-01 17:44:57,618 - Pasta_Align===
DEBUG   Number of species aligned: 45
===2016-12-01 17:44:57,620 - Pasta_Align===
DEBUG   bash /home/kate_crosby/BAD_Mutations/Shell_Scripts/Pasta_Align.sh /home/kate_crosby/BAD_Mutations/bm_test/lib/python2.7/site-packages/run_pasta.py /tmp/BAD_Mutations_PastaInput_LXpvLW.fasta /tmp pastajob_1480614297.619982

Basically after that last Pasta align with 'number of species aligned', the job just hangs (there's nothing in the output directory).

Not sure what could be going on here, but my understanding is I need the alignments and trees produced from this step (not as a messy log file or an obscurely named newick file in a tmp directory - where I didn't specify the output to go to).

An inspection of said /tmp directory reveals the following:

**pastajob_1480614297.619982**
pastajob_1480614297.619982.err.txt
pastajob_1480614297.619982.marker001.BAD_Mutations_PastaInput_LXpvLW.aln
pastajob_1480614297.619982.out.txt
pastajob_1480614297.619982.score.txt
pastajob_1480614297.619982_temp_iteration_initialsearch_seq_alignment.txt
pastajob_1480614297.619982_temp_iteration_initialsearch_seq_unmasked_alignment.gz
pastajob_1480614297.619982_temp_iteration_initialsearch_tree.tre
pastajob_1480614297.619982_temp_name_translation.txt
pastajob_1480614297.619982_temp_pasta_config.txt
pastajob_1480614297.619982.tre

The /tmp dir is owned by root (not me) - do I need sudo privileges (I won't get them) + (I'm on an obscure cloud system that is not like U Minn's system) to get pasta to write out from /tmp?

Can I redirect pasta to a local tmp? If so, file(s) + line number(s) would be helpful.

[kate-crosby]

It looks like it might have something more to do with the pasta dependency.

[TomJKono]

BAD_Mutations will copy the finished alignment and tree files from the temp directory as soon as the Pasta process finishes. I remember Pasta not handling stop codons well, but I think I fixed that in an earlier commit. I'm downloading the latest genome databases and trying to reproduce the issue!

[TomJKono]

Hello,

I have tried running BAD_Mutations on various setups, and am unable to reproduce the error! How did you set up pasta? I'd like to be able to account for the ways that pasta works in my setup. Thanks!