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pplacer error - related to concat.updated.gene_map file? #322

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hollybik opened this Issue Oct 10, 2012 · 5 comments

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hollybik commented Oct 10, 2012

Getting an error on yesterday's build of PhyloSift devel branch. Ran command on my iMac (but this input data is also on Edhar):

./phylosift.pl all ~/Desktop/PhyloSift/test_data/xeno_unassembled/xeno_raw_s_2_1_sequence.txt --debug

I built the xeno marker packages (but missing the taxon map), and tried runnning PhloSift to see if I was getting hits to the new markers. However, I got this error:

Removed 235 sequences on long pendant edges
Using markermap /Users/hollybik/share/phylosift/markers/concat.updated/concat.taxonmap
Reading taxonmap
Unable to read from /Users/hollybik/share/phylosift/markers/concat.updated/concat.updated.gene_map at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Utilities.pm line 85
Phylosift::Utilities::ps_open('/Users/hollybik/share/phylosift/markers/concat.updated/concat...') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 504
Phylosift::pplacer::read_name_map('marker', 'concat') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 522
Phylosift::pplacer::name_taxa_in_jplace('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'input', '/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS...', 'output', '/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS...', 'taxonmap', 'HASH(0x7fc12154ee08)', 'marker', ...) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 366
Phylosift::pplacer::place_reads('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker', 'concat', 'dna', 0, 'chunk', 1, 'reads', ...) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 80
Phylosift::pplacer::pplacer('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc121487a40)', 'chunk', 1) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/MarkerAlign.pm line 121
Phylosift::MarkerAlign::MarkerAlign('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc12135b358)', 'chunk', 1) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/FastSearch.pm line 141
Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc12135b358)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Phylosift.pm line 494
Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'cont', 0, 'marker', 'ARRAY(0x7fc12135b358)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Phylosift.pm line 188
Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x7fc121662f48)', 'force', undef, 'custom', undef, 'cont', undef) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Command/all.pm line 103
Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x7fc121685128)', 'Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x7fc12168fa70)', 'ARRAY(0x7fc12114bcf0)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/App/Cmd.pm line 243
App::Cmd::execute_command('Phylosift=HASH(0x7fc1211a3cc0)', 'Phylosift::Command::all=HASH(0x7fc121685128)', 'Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x7fc12168fa70)', '/Users/hollybik/Desktop/PhyloSift/test_data/xeno_unassembled/...') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/App/Cmd.pm line 171
App::Cmd::run('Phylosift') called at ./bin/phylosift line 8

@ghost ghost assigned gjospin Oct 10, 2012

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gjospin Oct 15, 2012

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What markers DB was used ?
Devel markers have the .gene_map file required for this part of the code.
Maybe it hadn't been updated at the time of the run.

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gjospin commented Oct 15, 2012

What markers DB was used ?
Devel markers have the .gene_map file required for this part of the code.
Maybe it hadn't been updated at the time of the run.

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hollybik Oct 15, 2012

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Re-downloaded newest version of phylosift and devel markers, and running xeno data now (after reindexing marker DB with xeno 18S marker added in). Will see if the error still pops up.

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hollybik commented Oct 15, 2012

Re-downloaded newest version of phylosift and devel markers, and running xeno data now (after reindexing marker DB with xeno 18S marker added in). Will see if the error still pops up.

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koadman Oct 22, 2012

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@hollybik Can we close this? I am not seeing similar errors on devel.

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koadman commented Oct 22, 2012

@hollybik Can we close this? I am not seeing similar errors on devel.

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hollybik Oct 23, 2012

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This might be a mac specific issue? or perhaps an issue with my xeno marker package? On October 9th's version of devel I was getting another error (below). I will re-download last night's devel build to see if I can still replicate this.

Running /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../osx/pplacer --groups 15 --mmap-file abracadabra -o /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS_temp/xeno_raw_s_2_1_sequence.txt/treeDir/concat.updated.1.jplace --verbosity 0 -j 1 -c /Users/hollybik/share/phylosift/markers/concat.updated "/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS_temp/xeno_raw_s_2_1_sequence.txt/alignDir/concat.updated.1.fasta"
Removed 235 sequences on long pendant edges
Using markermap /Users/hollybik/share/phylosift/markers/concat.updated/concat.taxonmap
Reading taxonmap
Unable to read from /Users/hollybik/share/phylosift/markers/concat.updated/concat.updated.gene_map at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Utilities.pm line 85
Phylosift::Utilities::ps_open('/Users/hollybik/share/phylosift/markers/concat.updated/concat...') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 504
Phylosift::pplacer::read_name_map('marker', 'concat') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 522
Phylosift::pplacer::name_taxa_in_jplace('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'input', '/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS...', 'output', '/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS...', 'taxonmap', 'HASH(0x7fc12154ee08)', 'marker', ...) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 366
Phylosift::pplacer::place_reads('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker', 'concat', 'dna', 0, 'chunk', 1, 'reads', ...) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 80
Phylosift::pplacer::pplacer('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc121487a40)', 'chunk', 1) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/MarkerAlign.pm line 121
Phylosift::MarkerAlign::MarkerAlign('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc12135b358)', 'chunk', 1) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/FastSearch.pm line 141
Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc12135b358)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Phylosift.pm line 494
Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'cont', 0, 'marker', 'ARRAY(0x7fc12135b358)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Phylosift.pm line 188
Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x7fc121662f48)', 'force', undef, 'custom', undef, 'cont', undef) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Command/all.pm line 103
Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x7fc121685128)', 'Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x7fc12168fa70)', 'ARRAY(0x7fc12114bcf0)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/App/Cmd.pm line 243
App::Cmd::execute_command('Phylosift=HASH(0x7fc1211a3cc0)', 'Phylosift::Command::all=HASH(0x7fc121685128)', 'Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x7fc12168fa70)', '/Users/hollybik/Desktop/PhyloSift/test_data/xeno_unassembled/...') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/App/Cmd.pm line 171
App::Cmd::run('Phylosift') called at ./bin/phylosift line 8

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hollybik commented Oct 23, 2012

This might be a mac specific issue? or perhaps an issue with my xeno marker package? On October 9th's version of devel I was getting another error (below). I will re-download last night's devel build to see if I can still replicate this.

Running /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../osx/pplacer --groups 15 --mmap-file abracadabra -o /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS_temp/xeno_raw_s_2_1_sequence.txt/treeDir/concat.updated.1.jplace --verbosity 0 -j 1 -c /Users/hollybik/share/phylosift/markers/concat.updated "/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS_temp/xeno_raw_s_2_1_sequence.txt/alignDir/concat.updated.1.fasta"
Removed 235 sequences on long pendant edges
Using markermap /Users/hollybik/share/phylosift/markers/concat.updated/concat.taxonmap
Reading taxonmap
Unable to read from /Users/hollybik/share/phylosift/markers/concat.updated/concat.updated.gene_map at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Utilities.pm line 85
Phylosift::Utilities::ps_open('/Users/hollybik/share/phylosift/markers/concat.updated/concat...') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 504
Phylosift::pplacer::read_name_map('marker', 'concat') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 522
Phylosift::pplacer::name_taxa_in_jplace('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'input', '/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS...', 'output', '/Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/PS...', 'taxonmap', 'HASH(0x7fc12154ee08)', 'marker', ...) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 366
Phylosift::pplacer::place_reads('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker', 'concat', 'dna', 0, 'chunk', 1, 'reads', ...) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/pplacer.pm line 80
Phylosift::pplacer::pplacer('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc121487a40)', 'chunk', 1) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/MarkerAlign.pm line 121
Phylosift::MarkerAlign::MarkerAlign('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc12135b358)', 'chunk', 1) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/FastSearch.pm line 141
Phylosift::FastSearch::run_search('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'marker_reference', 'ARRAY(0x7fc12135b358)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Phylosift.pm line 494
Phylosift::Phylosift::run_search('self', 'Phylosift::Phylosift=HASH(0x7fc121662f48)', 'cont', 0, 'marker', 'ARRAY(0x7fc12135b358)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Phylosift.pm line 188
Phylosift::Phylosift::run('Phylosift::Phylosift=HASH(0x7fc121662f48)', 'force', undef, 'custom', undef, 'cont', undef) called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/Phylosift/Command/all.pm line 103
Phylosift::Command::all::execute('Phylosift::Command::all=HASH(0x7fc121685128)', 'Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x7fc12168fa70)', 'ARRAY(0x7fc12114bcf0)') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/App/Cmd.pm line 243
App::Cmd::execute_command('Phylosift=HASH(0x7fc1211a3cc0)', 'Phylosift::Command::all=HASH(0x7fc121685128)', 'Getopt::Long::Descriptive::Opts::OPT::2=HASH(0x7fc12168fa70)', '/Users/hollybik/Desktop/PhyloSift/test_data/xeno_unassembled/...') called at /Users/hollybik/Desktop/PhyloSift/phylosift_devel_20121009/bin/../lib/App/Cmd.pm line 171
App::Cmd::run('Phylosift') called at ./bin/phylosift line 8

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gjospin Oct 29, 2012

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I think this went away in Friday's tests.

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gjospin commented Oct 29, 2012

I think this went away in Friday's tests.

@gjospin gjospin closed this Oct 29, 2012

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