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Legacy PATRIC Website (JBoss Portal Version)
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Comprehensive Genome Analysis: Figure 3 is missing from the report #2298

Open chmao1 opened 5 years ago

chmao1 commented 5 years ago

Figure 3 is missing from FullGenomeReport.html

image

nconrad commented 5 years ago

We think this was related to the Data API being down. @chmao1 did you confirm this no longer an issue?

chmao1 commented 5 years ago

This is still an issue. I reran the test after the DATA API came back last Friday and the figure 3 was still missing in the report.
Please see: https://beta.patricbrc.org/workspace/olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella%20enterica%20test_SRR2/FullGenomeReport.html

chmao1 commented 5 years ago

Job ID: 24272

Here is the error output:

Running process 18098 as task 1711 Executing under P3 shepherd 18095 Report headers from /olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella enterica test_SRR2/.assembly/39_analysis.zip: Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) # contigs Largest contig Total length GC (%) N50 N75 L50 L75 # N's per 100 kbpSetting contigs to assembled contigs at /olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella enterica test_SRR2/.assembly/contigs.fa Writing to tempdir /disks/tmp/RG6aIhhsns p3x-generate-circos generated truncation statistics: '90/90' /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|290338.8.peg.2689(M 0) does not correspond to fig|290338.8.peg.2689(gtg) % (pro.id, aa, aa_num, nucl.id, this_codon)) /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|295319.15.peg.3006(M 0) does not correspond to fig|295319.15.peg.3006(ttg) % (pro.id, aa, aa_num, nucl.id, this_codon)) /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|41514.7.peg.1(M 0) does not correspond to fig|41514.7.peg.1(gtg) % (pro.id, aa, aa_num, nucl.id, this_codon)) Jul 12, 2019 8:28:30 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:34 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:39 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:44 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:49 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:55 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Codon tree codon_tree/CodonTree.nex does not exist at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 562, <$fh> line 1. Bio::KBase::AppService::ComprehensiveGenomeAnalysis::compute_tree("annotation-with-stats.genome", "codon_tree", 10) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 426 Bio::KBase::AppService::ComprehensiveGenomeAnalysis::generate_report(Bio::KBase::AppService::ComprehensiveGenomeAnalysis=HASH(0x26cde50)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 107 Bio::KBase::AppService::ComprehensiveGenomeAnalysis::run(Bio::KBase::AppService::ComprehensiveGenomeAnalysis=HASH(0x26cde50), Bio::KBase::AppService::AppScript=HASH(0x4528200), HASH(0x3477568), HASH(0x3477598), HASH(0x345def8)) called at /vol/patric3/production/P3Slurm/deployment/plbin/App-ComprehensiveGenomeAnalysis.pl line 16 main::ANON(Bio::KBase::AppService::AppScript=HASH(0x4528200), HASH(0x3477568), HASH(0x3477598), HASH(0x345def8)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 402 eval {...} called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 401 Bio::KBase::AppService::AppScript::subproc_run(Bio::KBase::AppService::AppScript=HASH(0x4528200)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 276 Bio::KBase::AppService::AppScript::run(Bio::KBase::AppService::AppScript=HASH(0x4528200), ARRAY(0x26ce228)) called at /vol/patric3/production/P3Slurm/deployment/plbin/App-ComprehensiveGenomeAnalysis.pl line 18 Creating report with command: create-report -i annotation-with-stats.genome --n-contigs 90 --n-contigs-drawn 90 -o FullGenomeReport.html -c circos.svg -s subsystem_colors.json *** Could not read tree view file: undefined TypeError: path must be a string or Buffer at fs.readFile (fs.js:358:11) at internal/util.js:230:26 at buildReport (/vol/patric3/production/P3Slurm/deployment/lib/genome_report/scripts/create-report.js:109:25) at $VAR1 = [ [ 'Salmonella enterica test_SRR2', 'job_result', '/olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/', '2019-07-13T01:29:27Z', 'A740EBCA-A50D-11E9-87A2-27A3682E0674', 'cmao@patricbrc.org', 19137, {}, { 'inspection_started' => '2019-07-13T01:29:27Z', 'is_folder' => 0 }, 'w', 'n', '' ] ];

ARWattam commented 5 years ago

Shouldn’t the job ID be longer? Like fe7ab36d-5777-44da-8e0e-4df2224ff939 (one of my recent job ids)?

From: chmao1 notifications@github.com Reply-To: PATRIC3/patric3_website reply@reply.github.com Date: Thursday, July 18, 2019 at 10:06 AM To: PATRIC3/patric3_website patric3_website@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [PATRIC3/patric3_website] Comprehensive Genome Analysis: Figure 3 is missing from the report (#2298)

Job ID: 24272

Here is the error output:

Running process 18098 as task 1711 Executing under P3 shepherd 18095 Report headers from /olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella enterica test_SRR2/.assembly/39_analysis.zip: Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) # contigs Largest contig Total length GC (%) N50 N75 L50 L75 # N's per 100 kbpSetting contigs to assembled contigs at /olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella enterica test_SRR2/.assembly/contigs.fa Writing to tempdir /disks/tmp/RG6aIhhsns p3x-generate-circos generated truncation statistics: '90/90' /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|290338.8.peg.2689(M 0) does not correspond to fig|290338.8.peg.2689(gtg) % (pro.id, aa, aa_num, nucl.id, this_codon)) /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|295319.15.peg.3006(M 0) does not correspond to fig|295319.15.peg.3006(ttg) % (pro.id, aa, aa_num, nucl.id, this_codon)) /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|41514.7.peg.1(M 0) does not correspond to fig|41514.7.peg.1(gtg) % (pro.id, aa, aa_num, nucl.id, this_codon)) Jul 12, 2019 8:28:30 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:34 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:39 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:44 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:49 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Jul 12, 2019 8:28:55 PM java.util.prefs.FileSystemPreferences$1 run WARNING: java.io.IOException: Permission denied Exception in thread "Thread-1" java.lang.SecurityException: Could not lock User prefs. Lock file access denied. at java.util.prefs.FileSystemPreferences.checkLockFile0ErrorCode(FileSystemPreferences.java:937) at java.util.prefs.FileSystemPreferences.lockFile(FileSystemPreferences.java:925) at java.util.prefs.FileSystemPreferences.sync(FileSystemPreferences.java:729) at java.util.prefs.FileSystemPreferences.flush(FileSystemPreferences.java:824) at java.util.prefs.FileSystemPreferences.syncWorld(FileSystemPreferences.java:464) at java.util.prefs.FileSystemPreferences.access$1200(FileSystemPreferences.java:50) at java.util.prefs.FileSystemPreferences$4$1.run(FileSystemPreferences.java:442) Codon tree codon_tree/CodonTree.nex does not exist at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 562, <$fh> line 1. Bio::KBase::AppService::ComprehensiveGenomeAnalysis::compute_tree("annotation-with-stats.genome", "codon_tree", 10) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 426 Bio::KBase::AppService::ComprehensiveGenomeAnalysis::generate_report(Bio::KBase::AppService::ComprehensiveGenomeAnalysis=HASH(0x26cde50)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 107 Bio::KBase::AppService::ComprehensiveGenomeAnalysis::run(Bio::KBase::AppService::ComprehensiveGenomeAnalysis=HASH(0x26cde50), Bio::KBase::AppService::AppScript=HASH(0x4528200), HASH(0x3477568), HASH(0x3477598), HASH(0x345def8)) called at /vol/patric3/production/P3Slurm/deployment/plbin/App-ComprehensiveGenomeAnalysis.pl line 16 main::ANON(Bio::KBase::AppService::AppScript=HASH(0x4528200), HASH(0x3477568), HASH(0x3477598), HASH(0x345def8)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 402 eval {...} called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 401 Bio::KBase::AppService::AppScript::subproc_run(Bio::KBase::AppService::AppScript=HASH(0x4528200)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 276 Bio::KBase::AppService::AppScript::run(Bio::KBase::AppService::AppScript=HASH(0x4528200), ARRAY(0x26ce228)) called at /vol/patric3/production/P3Slurm/deployment/plbin/App-ComprehensiveGenomeAnalysis.pl line 18 Creating report with command: create-report -i annotation-with-stats.genome --n-contigs 90 --n-contigs-drawn 90 -o FullGenomeReport.html -c circos.svg -s subsystem_colors.json *** Could not read tree view file: undefined TypeError: path must be a string or Buffer at fs.readFile (fs.js:358:11) at internal/util.js:230:26 at buildReport (/vol/patric3/production/P3Slurm/deployment/lib/genome_report/scripts/create-report.js:109:25) at $VAR1 = [ [ 'Salmonella enterica test_SRR2', 'job_result', '/olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/', '2019-07-13T01:29:27Z', 'A740EBCA-A50D-11E9-87A2-27A3682E0674', 'cmao@patricbrc.orgmailto:cmao@patricbrc.org', 19137, {}, { 'inspection_started' => '2019-07-13T01:29:27Z', 'is_folder' => 0 }, 'w', 'n', '' ] ];

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chmao1 commented 5 years ago

This job was run on PATRIC beta site. It seems that the job id on beta site uses different ID assign system. This one has job id 24272 instead of a long id.

Also, I noticed that on the job result page, it says job ID is 1711, which is task ID. This is confusing.

image

@olsonanl Bob, could you check this?

chmao1 commented 5 years ago

Here is the display of the job ID on the job status page (Beta site)

image

ARWattam commented 5 years ago

Thanks. I sent to Bob. We’ll see what he comes up with.

From: chmao1 notifications@github.com Reply-To: PATRIC3/patric3_website reply@reply.github.com Date: Thursday, July 18, 2019 at 10:22 AM To: PATRIC3/patric3_website patric3_website@noreply.github.com Cc: "Wattam, Rebecca (arw3s)" wattam@virginia.edu, Comment comment@noreply.github.com Subject: Re: [PATRIC3/patric3_website] Comprehensive Genome Analysis: Figure 3 is missing from the report (#2298)

Here is the display of the job ID on the job status page (Beta site)

[image]https://user-images.githubusercontent.com/6361802/61465368-f03edd00-a945-11e9-82fa-1aa8090fa638.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/PATRIC3/patric3_website/issues/2298?email_source=notifications&email_token=ACXRS5AN34OF7MPNSLYJPF3QAB4DBA5CNFSM4ICPK3BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2IUOMA#issuecomment-512837424, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACXRS5DSW5NZ7SLK2D346LTQAB4DBANCNFSM4ICPK3BA.

olsonanl commented 5 years ago

This was a permissions problem on the p3 home directory on one of the servers. I've restarted the job, new ID is 24283

chmao1 commented 5 years ago

@olsonanl The job 24283 is complete. However, the figure 3 is still missing in the report. Here is the link to the report: https://beta.patricbrc.org/workspace/olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella%20enterica%20test_SRR2/FullGenomeReport.html

Here is the error message: Running process 23139 as task 1723 Executing under P3 shepherd 23136 Report headers from /olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella enterica test_SRR2/.assembly/41_analysis.zip: Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) # contigs Largest contig Total length GC (%) N50 N75 L50 L75 # N's per 100 kbpSetting contigs to assembled contigs at /olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/.Salmonella enterica test_SRR2/.assembly/contigs.fa Writing to tempdir /disks/tmp/Soy03LRaVe p3x-generate-circos generated truncation statistics: '90/90' /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|290338.8.peg.2689(M 0) does not correspond to fig|290338.8.peg.2689(gtg) % (pro.id, aa, aa_num, nucl.id, this_codon)) /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|295319.15.peg.3006(M 0) does not correspond to fig|295319.15.peg.3006(ttg) % (pro.id, aa, aa_num, nucl.id, this_codon)) /disks/patric-common/runtime/lib/python2.7/site-packages/Bio/codonalign/init.py:585: UserWarning: fig|41514.7.peg.1(M 0) does not correspond to fig|41514.7.peg.1(gtg) % (pro.id, aa, aa_num, nucl.id, this_codon)) Codon tree codon_tree/CodonTree.nex does not exist at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 562, <$fh> line 1. Bio::KBase::AppService::ComprehensiveGenomeAnalysis::compute_tree("annotation-with-stats.genome", "codon_tree", 10) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 426 Bio::KBase::AppService::ComprehensiveGenomeAnalysis::generate_report(Bio::KBase::AppService::ComprehensiveGenomeAnalysis=HASH(0xdd5e50)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/ComprehensiveGenomeAnalysis.pm line 107 Bio::KBase::AppService::ComprehensiveGenomeAnalysis::run(Bio::KBase::AppService::ComprehensiveGenomeAnalysis=HASH(0xdd5e50), Bio::KBase::AppService::AppScript=HASH(0x2c2ff78), HASH(0x1b7e250), HASH(0x1b7e280), HASH(0x1b63be0)) called at /vol/patric3/production/P3Slurm/deployment/plbin/App-ComprehensiveGenomeAnalysis.pl line 16 main::ANON(Bio::KBase::AppService::AppScript=HASH(0x2c2ff78), HASH(0x1b7e250), HASH(0x1b7e280), HASH(0x1b63be0)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 402 eval {...} called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 401 Bio::KBase::AppService::AppScript::subproc_run(Bio::KBase::AppService::AppScript=HASH(0x2c2ff78)) called at /vol/patric3/production/P3Slurm/deployment/lib/Bio/KBase/AppService/AppScript.pm line 276 Bio::KBase::AppService::AppScript::run(Bio::KBase::AppService::AppScript=HASH(0x2c2ff78), ARRAY(0xdd6228)) called at /vol/patric3/production/P3Slurm/deployment/plbin/App-ComprehensiveGenomeAnalysis.pl line 18 Creating report with command: create-report -i annotation-with-stats.genome --n-contigs 90 --n-contigs-drawn 90 -o FullGenomeReport.html -c circos.svg -s subsystem_colors.json *** Could not read tree view file: undefined TypeError: path must be a string or Buffer at fs.readFile (fs.js:358:11) at internal/util.js:230:26 at buildReport (/vol/patric3/production/P3Slurm/deployment/lib/genome_report/scripts/create-report.js:109:25) at $VAR1 = [ [ 'Salmonella enterica test_SRR2', 'job_result', '/olson@patricbrc.org/PATRIC-QA/applications/App-ComprehensiveGenomeAnalysis/', '2019-07-18T22:28:11Z', '5323BE26-A9AB-11E9-84D8-9FF0682E0674', 'cmao@patricbrc.org', 19568, {}, { 'inspection_started' => '2019-07-18T22:28:11Z', 'is_folder' => 0 }, 'w', 'n', '' ] ];