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Could you share a complete output using the --debug flag to know when the error occurs?It is possibly though I haven't looked at the code in a while that using --continue skips some variable population which creates the undefined value later in the code execution.
On Mon, Sep 26, 2016 at 9:11 PM, Zachary Stewart <mrhue...@gmail.com> wrote:
Hi guys,
I've recently been running Phylosift on a number of samples, though one was stopped after performing alignment of a chunk (#23) due to an issue with the high power computer cluster I was running this on. I've since tried to resume this by using the command...
"phylosift place --continue --threads 4 --output ./PS_temp/output_directory --paired file.1.fq file.2.fq"
...which to my understanding should work (?), but when I attempt this I receive an error as below.
"Can't call method "unlock" on an undefined value at /pkg/suse11/phylosift/1.0.1/bin../lib/Phylosift/Phylosift.pm line 187".
I am able to initiate a fresh run, so I was wondering if someone knew why I am receiving this error when I attempt to --continue this run. I noticed someone else has received this error previously (https://groups.google.com/forum/#!topic/phylosift/fQZgGZTfX94) though they received it at the end of a run where it was apparently not a problem. Can anyone lend a hand?
Thanks,
Zac.
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Chunk 29 sequences processed 22a841cff3a1975b2cccbb7872588b3d |
Chunk 29 Search completed |
Chunk 29 Align completed |
Chunk 29 Place completed |
Chunk 29 Summarize completed |
Chunk 30 sequences processed d3393615d5188505feb5a5c8671a048d |
Chunk 30 Search completed |
Chunk 30 Align completed |
Program run as: |
phylosift place --continue --debug --threads 4 --output ./output_dir --paired file.1.fq file.2.fq |
Marker database version: |
http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/markers.tgz |
1413946442 |
Update on this situation, my second attempt to run this on two of my samples has also crashed. The first time this crash was caused by not allocating enough RAM with my PBS job submission script, now it appears as though my job is crashing with the same "unlock" error after I processed 80-95 hours of these samples. The start of the error file for both of these are as such:
Phylosoft (v1.0.1) module loaded. |
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Located in /pkg/suse11/phylosift/1.0.1 |
Unable to read from /pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/18s_reps.cm at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 85 |
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Phylosift::Utilities::ps_open('/pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/...') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 840 |
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Phylosift::Utilities::get_marker_length('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker', '18s_reps') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 986 |
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Phylosift::FastSearch::write_candidates('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'hitsref', 'HASH(0x232fbd8)', 'searchtype', '.lastal.rna', 'reads', '/home/my_folder/output_dir/bla...', 'process_id', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 319 |
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Phylosift::FastSearch::launch_searches('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'readtype', 'HASH(0x120a168)', 'dir', '/home/my_folder/output_dir/bla...', 'contigs', 0, 'chunk', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 136 |
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Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker_reference', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 418 |
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Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'cont', 0, 'marker', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 175 |
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Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x2649f80)', 'force', undef, 'custom', undef, 'cont', undef) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Command/all.pm line 129 |
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Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'ARRAY(0xbfa678)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 243 |
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App::Cmd::execute_command('Phylosift=HASH(0x2638370)', 'Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'file.1.fq', 'file.2.fq') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 171 |
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App::Cmd::run('Phylosift') called at /pkg/suse11/phylosift/1.0.1/bin/phylosift line 7 |
---and---
Phylosoft (v1.0.1) module loaded. |
|
Located in /pkg/suse11/phylosift/1.0.1 |
Unable to read from /pkg/suse11/phylosift/1.0.1/share/phylosift/markers/16s_reps_bac/16s_reps_bac.cm at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 85 |
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Phylosift::Utilities::ps_open('/pkg/suse11/phylosift/1.0.1/share/phylosift/markers/16s_reps_...') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 840 |
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Phylosift::Utilities::get_marker_length('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker', '16s_reps_bac') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 986 |
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Phylosift::FastSearch::write_candidates('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'hitsref', 'HASH(0x232fbd8)', 'searchtype', '.lastal.rna', 'reads', '/home/my_folder/output_dir...', 'process_id', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 319 |
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Phylosift::FastSearch::launch_searches('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'readtype', 'HASH(0x120a168)', 'dir', '/home/my_folder/output_dir...', 'contigs', 0, 'chunk', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 136 |
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Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker_reference', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 418 |
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Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'cont', 0, 'marker', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 175 |
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Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x2649f80)', 'force', undef, 'custom', undef, 'cont', undef) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Command/all.pm line 129 |
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Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'ARRAY(0xbfa678)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 243 |
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App::Cmd::execute_command('Phylosift=HASH(0x2638370)', 'Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'file.1.fq', 'file.2.fq') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 171 |
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App::Cmd::run('Phylosift') called at /pkg/suse11/phylosift/1.0.1/bin/phylosift line 7 |
_________________________
The tail of these two are as such:
Unable to read from /pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/18s_reps.cm at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 85 |
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Phylosift::Utilities::ps_open('/pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/...') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 840 |
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Phylosift::Utilities::get_marker_length('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker', '18s_reps') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 986 |
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Phylosift::FastSearch::write_candidates('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'hitsref', 'HASH(0x232fbd8)', 'searchtype', '.lastal.rna', 'reads', '/home/my_folder/output_dir/bla...', 'process_id', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 319 |
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Phylosift::FastSearch::launch_searches('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'readtype', 'HASH(0x120a168)', 'dir', '/home/my_folder/output_dir/bla...', 'contigs', 0, 'chunk', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 136 |
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Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker_reference', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 418 |
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Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'cont', 0, 'marker', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 175 |
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Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x2649f80)', 'force', undef, 'custom', undef, 'cont', undef) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Command/all.pm line 129 |
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Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'ARRAY(0xbfa678)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 243 |
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App::Cmd::execute_command('Phylosift=HASH(0x2638370)', 'Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'file.1.fq', 'file.2.fq') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 171 |
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App::Cmd::run('Phylosift') called at /pkg/suse11/phylosift/1.0.1/bin/phylosift line 7 |
Can't call method "unlock" on an undefined value at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 187. |
---and---
Unable to read from /pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/18s_reps.cm at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 85 |
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Phylosift::Utilities::ps_open('/pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/...') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Utilities.pm line 840 |
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Phylosift::Utilities::get_marker_length('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker', '18s_reps') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 986 |
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Phylosift::FastSearch::write_candidates('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'hitsref', 'HASH(0x232fbd8)', 'searchtype', '.lastal.rna', 'reads', '/home/my_folder/output_dir...', 'process_id', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 319 |
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Phylosift::FastSearch::launch_searches('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'readtype', 'HASH(0x120a168)', 'dir', '/home/my_folder/output_dir...', 'contigs', 0, 'chunk', ...) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/FastSearch.pm line 136 |
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Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'marker_reference', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 418 |
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Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x2649f80)', 'cont', 0, 'marker', 'ARRAY(0x24e49f0)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 175 |
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Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x2649f80)', 'force', undef, 'custom', undef, 'cont', undef) called at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Command/all.pm line 129 |
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Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'ARRAY(0xbfa678)') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 243 |
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App::Cmd::execute_command('Phylosift=HASH(0x2638370)', 'Phylosift::Command::all=HASH(0x2661f18)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x272d938)', 'file.1.fq', 'file.2.fq') called at /pkg/suse11/phylosift/1.0.1/bin/../lib/App/Cmd.pm line 171 |
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App::Cmd::run('Phylosift') called at /pkg/suse11/phylosift/1.0.1/bin/phylosift line 7 |
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Uncaught exception: Failure("Sequence 925132.2.1.99 doesn't overlap any reference sequences.") |
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Fatal error: exception Failure("Sequence 925132.2.1.99 doesn't overlap any reference sequences.") |
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Uncaught exception: Failure("Sequence 301650.1.2.88 doesn't overlap any reference sequences.") |
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Fatal error: exception Failure("Sequence 301650.1.2.88 doesn't overlap any reference sequences.") |
Can't call method "unlock" on an undefined value at /pkg/suse11/phylosift/1.0.1/bin/../lib/Phylosift/Phylosift.pm line 187. |
______________________
I did not run these with the --debug tag so I don't have detailed output logs.
I will need to contact my computer cluster's support to see if this is
something they might understand. For now it seems like Phylosift might not be
capable of running these jobs, as many of them are expected to take upwards of
800 hours and I cannot be certain they won't crash at any moment. If you can
help with figuring this out still that would help as I think Phylosift provides
the best output for my study.
Thanks,
Zac.
Unable to read from /pkg/suse11/phylosift/1.0.1/share/phylosift/markers/18s_reps/18s_reps.cm |
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