test failures post install (tried both locally and with docker, same error)

[baverso]

Hello, I've installed topcons2 locally with all dependencies and executed the test command as described by the README in this git. The test command I'm referring to is
../run_topcons2.sh one_seq.fasta -outpath rst1

I received a pretty large output with several errors, where bash scripts exit with status 1, meaning an error had occurred but the details are not printed. I figured it could be an install issue or a dependency triggering the error so I tried to run topcons2 through a docker image instead, but the same output appeared when I ran the test command.

The output with the errors follows:
`user@64d5f15c4ea9:/app/topcons2/test$ ../run_topcons2.sh one_seq.fasta -outpath rst1
../workflow/pfam_workflow.py one_seq.fasta rst1/one_seq ../tools/blast-2.2.26/ ../database/blast/uniref90.fasta
cmdline: ./fa2prfs_pfamscan_v2.sh /tmp/seq_0_Uh23PG/ /app/topcons2/tools/blast-2.2.26
errmsg: Command '['./fa2prfs_pfamscan_v2.sh', '/tmp/seq_0_Uh23PG/', '/app/topcons2/tools/blast-2.2.26']' returned non-zero exit status 1
rmsg:

cmdline: ./fa2prfs_hmmscan.sh /tmp/seq_cdd_0_Ob9ofM/ /app/topcons2/tools/blast-2.2.26

errmsg: Command '['./fa2prfs_hmmscan.sh', '/tmp/seq_cdd_0_Ob9ofM/', '/app/topcons2/tools/blast-2.2.26']' returned non-zero exit status 1
rmsg:

cmdline: ./fa2prfs_fallback_v2.sh /tmp/seq_uniref_0_Skz9u9/ /app/topcons2/tools/blast-2.2.26 /app/topcons2/database/blast/uniref90.fasta
/tmp/runPhilius_DZs6Et04W
Command '['./fa2prfs_fallback_v2.sh', '/tmp/seq_uniref_0_Skz9u9/', '/app/topcons2/tools/blast-2.2.26', '/app/topcons2/database/blast/uniref90.fasta']' returned non-zero exit status 1

Final working dir: tmpdir= /tmp/seq_uniref_0_Skz9u9/
could not open prffile for query at ./bin/prf2NN_input_fast_scoring.pl line 35, line 1.
/bin/cp: cannot stat '/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf': No such file or directory
/bin/cp: cannot stat '/tmp/seq_uniref_0_Skz9u9/RAW_PRF_FILES//query.prf': No such file or directory
could not open prffile for query at ./bin/prf2NN_input_fast_scoring.pl line 35, line 1.
could not open prffile for query at ./bin/prf2NN_input_fast_scoring.pl line 35, line 1.
could not open prffile (/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
Opened file /tmp/seq_uniref_0_Skz9u9//DGHMM_KR_21_multi.txt for reading hmm names
Opened file /tmp/seq_uniref_0_Skz9u9//query.raw.prf.snf for reading sequence names
Opened file replacement_letter_multi.rpl for reading replacement letters
could not open prffile (/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
/tmp/seq_uniref_0_Skz9u9//query.raw.prf: No such file or directory
could not open prffile (/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile (/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile for query at ./bin/prf2KR_WY_NN_input_scoring.pl line 39, line 1.
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile for query at ./bin/prf2KR_WY_NN_input_scoring.pl line 39, line 1.
could not open prffile for query at ./bin/NN_pred2prf_2.pl line 47, line 1.
query
query
could not open prffile (/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
-:6: parser error : expected '>'

^
-:7: parser error : Opening and ending tag mismatch: seqs line 4 and hmm

^
could not open prffile for query at ./bin/NN_pred2prf_2.pl line 47, line 1.
-:8: parser error : expected '>'

^
-:9: parser error : Premature end of data in tag hmms line 1
unable to parse -
could not open prffile (/tmp/seq_uniref_0_Skz9u9/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
query
query
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin.txt for reading hmm names
Opened file /tmp/OCTOPUS_66jkCKiCNB/HMM_seqfiles.txt for reading sequence names
Opened file ./util/replacement_letter_multi.rpl for reading replacement letters
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
could not open prffile (/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, line 1.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Opened file ./HMM_FILES/spoctopus.txt for reading hmm names
Opened file /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/SIGPEP_HMM_SEQFILES.txt for reading sequence names
Running seq /tmp/OCTOPUS_66jkCKiCNB/HMM_PROFILES_2_ALPHA/query.prf on HMMS/NNZHMM_io_reent_hairpin.hmg
scoring ...
modhmms_octopus: /app/topcons2/predictors/source/modhmm/src/c/std_funcs.c:880: get_viterbi_label_path_length_multi: Assertion p_el' failed. Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin_sigpep.txt for reading hmm names Opened file /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/HMM_seqfiles.txt for reading sequence names Running seq /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/HMM_PROFILES_2_ALPHA/query.prf on HMMS/NNZHMM_io_reent_hairpin_sigpep.hmg scoring ... modhmms_spoctopus: /app/topcons2/predictors/source/modhmm/src/c/std_funcs.c:880: get_viterbi_label_path_length_multi: Assertion p_el' failed.

------------- EXCEPTION -------------
MSG: File does not exist '/tmp/seq_uniref_0_Skz9u9//query.hits.db'
STACK Bio::Index::Abstract::make_index /usr/local/share/perl/5.22.1/Bio/Index/Abstract.pm:577
STACK main::create_index ./blastget:109
STACK toplevel ./blastget:138

[blastall] WARNING: Unable to open query.hits.db.pin
[blastall] WARNING: Unable to open query.hits.db.pin
[blastall] WARNING: query: Unable to open query.hits.db.pin
[blastall] WARNING: query: Unable to open query.hits.db.pin

------------- EXCEPTION -------------
MSG: blastall call crashed: 256 | No such file or directory | /app/topcons2/tools/blast-2.2.26/bin/blastall -b 500 -a 4 -p blastp -e 1e-5 -o /tmp/lPEO1SKzyt -d "/data/topcons2_database/blast/tmp/seq_uniref_0_Skz9u9/query.hits.db" -i /tmp/K8seKcIhSU

STACK Bio::Tools::Run::StandAloneNCBIBlast::_runblast /usr/local/share/perl/5.22.1/Bio/Tools/Run/StandAloneNCBIBlast.pm:441
STACK Bio::Tools::Run::StandAloneNCBIBlast::_generic_local_blast /usr/local/share/perl/5.22.1/Bio/Tools/Run/StandAloneNCBIBlast.pm:411
STACK Bio::Tools::Run::StandAloneNCBIBlast::blastall /usr/local/share/perl/5.22.1/Bio/Tools/Run/StandAloneNCBIBlast.pm:263
STACK main::local_blast blastget:74
STACK toplevel blastget:170

jPhobius version 1.04
based on Phobius (c) Lukas Kall, Anders Krogh and Erik Sonnhammer 2004
and HomologHMM ver 1.04 (c) Lukas Kall 2005
Aborted (core dumped)
Aborted (core dumped)
-:11: parser error : Premature end of data in tag getScores line 9
-:11: parser error : Premature end of data in tag seq line 7
-:11: parser error : Premature end of data in tag seqs line 6
-:11: parser error : Premature end of data in tag hmm line 2
-:11: parser error : Premature end of data in tag hmms line 1
unable to parse -
-:11: parser error : Premature end of data in tag getScores line 9
-:11: parser error : Premature end of data in tag seq line 7
-:11: parser error : Premature end of data in tag seqs line 6
-:11: parser error : Premature end of data in tag hmm line 2
-:11: parser error : Premature end of data in tag hmms line 1
unable to parse -
could not open /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/DETAILED_TOPOLOGY_FILES//query.top at ./bin/lonely_revise_sigpep.pl line 62.
could not open /tmp/OCTOPUS_66jkCKiCNB/DETAILED_TOPOLOGY_FILES//query.top at ./bin/lonely_revise.pl line 62.
could not open /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/DETAILED_TOPOLOGY_FILES//query.top at ./bin/lonely_revise_sigpep.pl line 62.
could not open /tmp/OCTOPUS_66jkCKiCNB/HMM_PROFILES_MIOGR_lonely_revised/query.prf at ./bin/merge_HMM_profile_files.pl line 32, line 1.
/bin/ls: cannot access '/tmp/OCTOPUS_66jkCKiCNB/HMM_PROFILES_2_ALPHA_lonely_revised/': No such file or directory
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin.txt for reading hmm names
Opened file /tmp/OCTOPUS_66jkCKiCNB/HMM_seqfiles.txt for reading sequence names
Opened file ./util/replacement_letter_multi.rpl for reading replacement letters
could not open /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/HMM_PROFILES_MIOGR_lonely_revised/query.prf at ./bin/merge_HMM_profile_files.pl line 32, line 1.
could not open /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/HMM_PROFILES_MIOGR_lonely_revised/query.prf at ./bin/merge_HMM_profile_files.pl line 32, line 1.
/bin/ls: cannot access '/tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/HMM_PROFILES_2_ALPHA_lonely_revised/': No such file or directory
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin_sigpep.txt for reading hmm names
Opened file /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/HMM_seqfiles.txt for reading sequence names
could not open /tmp/OCTOPUS_66jkCKiCNB/DETAILED_TOPOLOGY_FILES_lr/query.top at ./bin/post_process_preds.pl line 22, line 1.
/bin/cp: cannot stat '/tmp/OCTOPUS_66jkCKiCNB/DETAILED_TOPOLOGY_FILES_final/query.top': No such file or directory
can't open fasta file at oneline.pl line 6.
rm: cannot remove '/app/topcons2/test/rst1/one_seq/seq_0//OCTOPUS/OCTOPUS.top.tmp': No such file or directory
/bin/cp: cannot stat '/tmp/OCTOPUS_66jkCKiCNB/HMM_PROFILES_2_ALPHA_lonely_revised/query.prf': No such file or directory
could not open /tmp/SPOCTOPUS_nv4zImmBGc/spoctopus_tmp_query/TEMP/DETAILED_TOPOLOGY_FILES_lr/query.top at ./bin/post_process_preds.pl line 22, line 1.
/bin/cp: cannot stat '/tmp/SPOCTOPUS_nv4zImmBGc/PREDICTED_DETAILED_TOPOLOGY_FILES/query.top': No such file or directory
can't open fasta file at oneline_sp.pl line 6.
rm: cannot remove '/app/topcons2/test/rst1/one_seq/seq_0//SPOCTOPUS/SPOCTOPUS.top.tmp': No such file or directory
Traceback (most recent call last):
File "../workflow/pfam_workflow.py", line 404, in
sys.exit(main(sys.argv, g_params))
File "../workflow/pfam_workflow.py", line 361, in main
with open(tmpDir + "query.hits.db") as inFile:
IOError: [Errno 2] No such file or directory: '/tmp/seq_uniref_0_Skz9u9/query.hits.db'`

[nanjiangshu]

Hi @baverso ,

It seems your docker container has not been started correctly.
How did you started your container? Exactly following the README by

 docker run -v /data/topcons2_database:/data/topcons2_database -it nanjiang/topcons2

What does the output of your

tree /data/topcons2_database

[ramou]

I believe the OP is indicating that they installed locally, as in they're not using the docker image. I've done the same thing and have what appears to be the same error if I haven't put the "database" directory (the 55GB zip) under topcons2_webserver. While I'm 99% sure that's the cause here, it would be nice to die with a useful error if the database part of the software isn't installed, and that may be the source of the confusion.

[ramou]

I can confirm that I could duplicate what the OP did and that linking to the database indicated in the install instructions made the problem go away. I believe this issue can be closed, but reiterate that a message regarding the database not being there would be nice.

[crpsalazar]

I'm getting a similar issue but this time with Singularity. In this case, I have the database in /databases/topcons2_database and ran this command:

simg=/tools/software/bioinfo-tools/protein_prediction/topcon/TOPCONS2/topcons2.img
singularity exec -B /databases:/data -B /work $simg /app/topcons2/run_topcons2.sh /app/topcons2/test/one_seq.fasta -outpath /work/csalazar/topcons/scratch/rst1

I get this error message:

/app/topcons2/workflow/pfam_workflow.py /app/topcons2/test/one_seq.fasta /work/csalazar/topcons/scratch/rst1/one_seq /app/topcons2/tools/blast-2.2.26/ /app/topcons2/database/blast/uniref90.fasta 

/tmp/runPhilius_1wrJPyLLZ
cmdline:  ./fa2prfs_pfamscan_v2.sh /tmp/seq_0_uPQ_RX/ /app/topcons2/tools/blast-2.2.26
errmsg: Command '['./fa2prfs_pfamscan_v2.sh', '/tmp/seq_0_uPQ_RX/', '/app/topcons2/tools/blast-2.2.26']' returned non-zero exit status 1
rmsg: 

cmdline: ./fa2prfs_hmmscan.sh /tmp/seq_cdd_0_ktMtfB/ /app/topcons2/tools/blast-2.2.26
errmsg: Command '['./fa2prfs_hmmscan.sh', '/tmp/seq_cdd_0_ktMtfB/', '/app/topcons2/tools/blast-2.2.26']' returned non-zero exit status 1
rmsg: 

cmdline: ./fa2prfs_fallback_v2.sh /tmp/seq_uniref_0_xtiitB/ /app/topcons2/tools/blast-2.2.26 /app/topcons2/database/blast/uniref90.fasta
Command '['./fa2prfs_fallback_v2.sh', '/tmp/seq_uniref_0_xtiitB/', '/app/topcons2/tools/blast-2.2.26', '/app/topcons2/database/blast/uniref90.fasta']' returned non-zero exit status 1

Final working dir: tmpdir= /tmp/seq_uniref_0_xtiitB/

could not open prffile for query at ./bin/prf2NN_input_fast_scoring.pl line 35, <PROTNAMEFILE> line 1.
/bin/cp: cannot stat '/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf': No such file or directory
/bin/cp: cannot stat '/tmp/seq_uniref_0_xtiitB/RAW_PRF_FILES//query.prf': No such file or directory
could not open prffile for query at ./bin/prf2NN_input_fast_scoring.pl line 35, <PROTNAMEFILE> line 1.
could not open prffile for query at ./bin/prf2NN_input_fast_scoring.pl line 35, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
Opened file /tmp/seq_uniref_0_xtiitB//DGHMM_KR_21_multi.txt for reading hmm names
Opened file /tmp/seq_uniref_0_xtiitB//query.raw.prf.snf for reading sequence names
Opened file replacement_letter_multi.rpl for reading replacement letters
could not open prffile (/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
/tmp/seq_uniref_0_xtiitB//query.raw.prf: No such file or directory
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile for query at ./bin/prf2KR_WY_NN_input_scoring.pl line 39, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile for query at ./bin/prf2KR_WY_NN_input_scoring.pl line 39, <PROTNAMEFILE> line 1.
-:6: parser error : expected '>'
</seqs>
     ^
-:7: parser error : Opening and ending tag mismatch: seqs line 4 and hmm
</hmm>
      ^
-:8: parser error : expected '>'
</hmms>
     ^
-:9: parser error : Premature end of data in tag hmms line 1
unable to parse -
could not open prffile for query at ./bin/NN_pred2prf_2.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile for query at ./bin/NN_pred2prf_2.pl line 47, <PROTNAMEFILE> line 1.
query
query
query
query
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.

------------- EXCEPTION -------------
MSG: File does not exist '/tmp/seq_uniref_0_xtiitB//query.hits.db'
STACK Bio::Index::Abstract::make_index /usr/local/share/perl/5.22.1/Bio/Index/Abstract.pm:577
STACK main::create_index ./blastget:109
STACK toplevel ./blastget:138
-------------------------------------

could not open prffile (/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/PSSMDIR/query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
could not open prffile (/tmp/seq_uniref_0_xtiitB/PSSM_PRF_FILES//query.prf) for query at ./bin/NN_pred2prf.pl line 47, <PROTNAMEFILE> line 1.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Use of uninitialized value within @cols in array dereference at ./bin/make_simple_sigpep_pred.pl line 52.
Use of uninitialized value $col[2] in numeric eq (==) at ./bin/make_simple_sigpep_pred.pl line 53.
Opened file ./HMM_FILES/spoctopus.txt for reading hmm names
Opened file /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/SIGPEP_HMM_SEQFILES.txt for reading sequence names
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin.txt for reading hmm names
Opened file /tmp/OCTOPUS_Hb97QEADK1/HMM_seqfiles.txt for reading sequence names
Opened file ./util/replacement_letter_multi.rpl for reading replacement letters
Running seq /tmp/OCTOPUS_Hb97QEADK1/HMM_PROFILES_2_ALPHA/query.prf on HMMS/NNZHMM_io_reent_hairpin.hmg
scoring ...
modhmms_octopus: /app/topcons2/predictors/source/modhmm/src/c/std_funcs.c:880: get_viterbi_label_path_length_multi: Assertion `p_el' failed.
Aborted
-:11: parser error : Premature end of data in tag getScores line 9
-:11: parser error : Premature end of data in tag seq line 7
-:11: parser error : Premature end of data in tag seqs line 6
-:11: parser error : Premature end of data in tag hmm line 2
-:11: parser error : Premature end of data in tag hmms line 1
unable to parse -
could not open /tmp/OCTOPUS_Hb97QEADK1/DETAILED_TOPOLOGY_FILES//query.top at ./bin/lonely_revise.pl line 62.
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin_sigpep.txt for reading hmm names
Opened file /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/HMM_seqfiles.txt for reading sequence names
could not open /tmp/OCTOPUS_Hb97QEADK1/HMM_PROFILES_MIOGR_lonely_revised/query.prf at ./bin/merge_HMM_profile_files.pl line 32, <PROTNAMEFILE> line 1.
/bin/ls: cannot access '/tmp/OCTOPUS_Hb97QEADK1/HMM_PROFILES_2_ALPHA_lonely_revised/*': No such file or directory
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin.txt for reading hmm names
Opened file /tmp/OCTOPUS_Hb97QEADK1/HMM_seqfiles.txt for reading sequence names
Opened file ./util/replacement_letter_multi.rpl for reading replacement letters
Running seq /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/HMM_PROFILES_2_ALPHA/query.prf on HMMS/NNZHMM_io_reent_hairpin_sigpep.hmg
scoring ...
modhmms_spoctopus: /app/topcons2/predictors/source/modhmm/src/c/std_funcs.c:880: get_viterbi_label_path_length_multi: Assertion `p_el' failed.
Aborted
-:11: parser error : Premature end of data in tag getScores line 9
-:11: parser error : Premature end of data in tag seq line 7
-:11: parser error : Premature end of data in tag seqs line 6
-:11: parser error : Premature end of data in tag hmm line 2
-:11: parser error : Premature end of data in tag hmms line 1
unable to parse -
could not open /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/DETAILED_TOPOLOGY_FILES//query.top at ./bin/lonely_revise_sigpep.pl line 62.
could not open /tmp/OCTOPUS_Hb97QEADK1/DETAILED_TOPOLOGY_FILES_lr/query.top at ./bin/post_process_preds.pl line 22, <PROTNAMEFILE> line 1.
could not open /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/DETAILED_TOPOLOGY_FILES//query.top at ./bin/lonely_revise_sigpep.pl line 62.
/bin/cp: cannot stat '/tmp/OCTOPUS_Hb97QEADK1/DETAILED_TOPOLOGY_FILES_final/query.top': No such file or directory
could not open /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/HMM_PROFILES_MIOGR_lonely_revised/query.prf at ./bin/merge_HMM_profile_files.pl line 32, <PROTNAMEFILE> line 1.
can't open fasta file at oneline.pl line 6.
could not open /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/HMM_PROFILES_MIOGR_lonely_revised/query.prf at ./bin/merge_HMM_profile_files.pl line 32, <PROTNAMEFILE> line 1.
/bin/ls: cannot access '/tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/HMM_PROFILES_2_ALPHA_lonely_revised/*': No such file or directory
rm: cannot remove '/work/csalazar/topcons/scratch/rst1/one_seq/seq_0//OCTOPUS/OCTOPUS.top.tmp': No such file or directory
Opened file ./HMM_FILES/NNZHMM_io_reent_hairpin_sigpep.txt for reading hmm names
Opened file /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/HMM_seqfiles.txt for reading sequence names
/bin/cp: cannot stat '/tmp/OCTOPUS_Hb97QEADK1/HMM_PROFILES_2_ALPHA_lonely_revised/query.prf': No such file or directory
[blastall] WARNING: Unable to open query.hits.db.pin
[blastall] WARNING: Unable to open query.hits.db.pin
[blastall] WARNING: query: Unable to open query.hits.db.pin
[blastall] WARNING: query: Unable to open query.hits.db.pin

------------- EXCEPTION -------------
MSG: blastall call crashed: 256 | No such file or directory | /app/topcons2/tools/blast-2.2.26/bin/blastall -i /tmp/bkfleQTQzX -b 500 -e 1e-5 -p blastp -a 4 -d "/data/topcons2_database/blast/tmp/seq_uniref_0_xtiitB/query.hits.db" -o \/tmp\/e2VF0nChEG

STACK Bio::Tools::Run::StandAloneNCBIBlast::_runblast /usr/local/share/perl/5.22.1/Bio/Tools/Run/StandAloneNCBIBlast.pm:441
STACK Bio::Tools::Run::StandAloneNCBIBlast::_generic_local_blast /usr/local/share/perl/5.22.1/Bio/Tools/Run/StandAloneNCBIBlast.pm:411
STACK Bio::Tools::Run::StandAloneNCBIBlast::blastall /usr/local/share/perl/5.22.1/Bio/Tools/Run/StandAloneNCBIBlast.pm:263
STACK main::local_blast blastget:74
STACK toplevel blastget:170
-------------------------------------

could not open /tmp/SPOCTOPUS_R9wkFz6zAe/spoctopus_tmp_query/TEMP/DETAILED_TOPOLOGY_FILES_lr/query.top at ./bin/post_process_preds.pl line 22, <PROTNAMEFILE> line 1.
/bin/cp: cannot stat '/tmp/SPOCTOPUS_R9wkFz6zAe/PREDICTED_DETAILED_TOPOLOGY_FILES/query.top': No such file or directory
can't open fasta file at oneline_sp.pl line 6.
rm: cannot remove '/work/csalazar/topcons/scratch/rst1/one_seq/seq_0//SPOCTOPUS/SPOCTOPUS.top.tmp': No such file or directory
jPhobius version 1.04
based on Phobius (c) Lukas Kall, Anders Krogh and Erik Sonnhammer 2004
and HomologHMM ver 1.04 (c) Lukas Kall 2005
Traceback (most recent call last):
  File "/app/topcons2/workflow/pfam_workflow.py", line 404, in <module>
    sys.exit(main(sys.argv, g_params))
  File "/app/topcons2/workflow/pfam_workflow.py", line 361, in main
    with open(tmpDir + "query.hits.db") as inFile:
IOError: [Errno 2] No such file or directory: '/tmp/seq_uniref_0_xtiitB/query.hits.db'

And these are the topologies inside the resulting query.result.txt:

TOPCONS predicted topology:
***No topology could be produced with this method***


OCTOPUS predicted topology:
***No topology could be produced with this method***


Philius predicted topology:
oooooooooooooooooppppppppppppppppppppiiiiiiiiiiiipppppppppppppppppppppppooooooooooooooooopppppppppppppppppppiiiiiiipppppppppppppppppppppooooooppppppppppppppppppppppiiiiiiiiiiiiiiiiippppppppppppppppppppooooooooooooppppppppppppppppppppiiiiiiiiiiiiiiiii


PolyPhobius predicted topology:
oooooooooooooooooopppppppppppppppppppiiiiiiiiiiipppppppppppppppppppppppooooooooooooooooppppppppppppppppppppppiiiiiippppppppppppppppppppppoooooppppppppppppppppppppiiiiiiiiiiiiiiiiiiiipppppppppppppppppppppooooooooooppppppppppppppppppppiiiiiiiiiiiiiiiii


SCAMPI predicted topology:
***No topology could be produced with this method***


SPOCTOPUS predicted topology:
***No topology could be produced with this method***


4fbzA:
---------oooooooooMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMoooooooooooooooooMMMMMMMMMMMMMMMMMMMMiiiiiiiMMMMMMMMMMMMMMMMMMMMMoooooooMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiiMMMMMMMMMMMMMMMMMMMMMooooooooooooMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiiiiiii

[ramou]

I think it may be your bind. I believe, as described, it should be:

singularity exec -B /databases/topcons2_database:/data -B /work $simg /app/topcons2/run_topcons2.sh /app/topcons2/test/one_seq.fasta -outpath /work/csalazar/topcons/scratch/rst1

Note that I bind the topcons2 database, not the directory above.

I've never used their singularity image, but I did roll this repo into our lab's singularity image and arrived at the same reasoning. I believe they'll have a symlink in their image from inside /app/topcons2/database to /data and if you shell in and look inside at what it's trying to run, it's a script in the "database", and so the path it's building isn't getting there... anyway, that's my best pre-coffee guess.

[arneelof]

I think you are correct. Most likely a bind issue.. Yours Arne

…

----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: arne@bioinfo.se 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751

On Sun, Jul 12, 2020 at 3:28 PM Stuart Thiel ***@***.***> wrote: I think it may be your bind. I believe, as described, it should be: singularity exec -B /databases/topcons2_database:/data -B /work $simg /app/topcons2/run_topcons2.sh /app/topcons2/test/one_seq.fasta -outpath /work/csalazar/topcons/scratch/rst1 Note that I bind the topcons2 database, not the directory above. I've never used their singularity image, but I did roll this repo into our lab's singularity image and arrived at the same reasoning. I believe they'll have a symlink in their image from inside /app/topcons2/database to /data and if you shell in and look inside at what it's trying to run, it's a script in the "database", and so the path it's building isn't getting there... anyway, that's my best pre-coffee guess. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA3LGSLU2A2QGBJAVWP7IBTR3G25BANCNFSM4JOB6E2A> .

[nanjiangshu]

Hi @crpsalazar

You command is correct. It should be -B /databases:/data if you have you topcons2 database at /databases/topcons2_database. I have just tested and it run well.

1. Have you pulled the latest image?
2. What is the content of your folder /databases/topcons2_database? It should contains
   blast cdd cdd_hmm pfam pfamfull pfam_seq
   If you have used symlinks in the database, you have to bind the real path (or the parent path) as well.

Best,
Nanjiang

[crpsalazar]

Hi @nanjiangshu,

1. I pulled the latest image again using singularity pull topcons2.img docker://nanjiang/topcons2, but the same error still occurs.
2. /databases/topcons2_database does contain blast cdd cdd_hmm pfam pfamfull pfam_seq, and none of these are symlinks.

I also @ramou's suggestion but same error also.

Cheers,
Carl

[nanjiangshu]

Hi @crpsalazar,

It is difficult to find what the problem is without knowing details of your system since I have never encountered the errors occurred to you. It could be related to the OS. For example, I have never tested TOPCONS with Singularity on Windows since I don't have one.

Maybe the easiest would be that I create a virtual machine for you and you login to the VM and setup TOPCONS singularity as you have done on your system. When you encounter similar problems again, I can login to VM to check what the problem is. If you can send me your public ssh key, I will send you instructions to login to the VM.

Best,

Nanjiang

[crpsalazar]

Hi @nanjiangshu,

Sorry for the late update. We were able to troubleshoot it, and found that it was related to slurm. There was no problem with the singularity image after all.

Cheers,
Carl

[nanjiangshu]

Hi @crpsalazar

Great that the problem is solved.

Best,

Nanjiang