test plant_tribes_kaks_analysis 1.0.3.0 #49

jennaj · 2022-07-15T18:53:59Z

Missing dependency reported:

/usr/local/bin/ruby: error while loading shared libraries: libjemalloc.so.1: cannot open shared object file: No such file or directory

toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0

jennaj · 2022-07-15T18:54:25Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0

mvdbeek · 2022-07-15T19:18:26Z

Results (powered by Planemo)

Summary

State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis (Test tool test #1)

Problems:

Output output_species1_paralog:  different than expected, difference (using contains):
( /tmp/tmpbjlxk588output_blastn_results1.tabular v. /tmp/tmpodxkmn8woutput_blastn_results1.tabular )
Failed to find 'contig_1;	contig_1;	100.00	346	0	0	1	346	1	346	0.0	640' in history data. (lines_diff=0).

Output output_rbhb_paralog:  different than expected, difference (using diff):
( /tmp/tmpk2agwkg6output_paralogous_pairs.tabular v. /tmp/tmpojwj55bdoutput_paralogous_pairs.tabular )
--- local_file
+++ history_data
@@ -1,3 +1,3 @@
-contig_241;	contig_241
+contig_241	contig_241;
+contig_586	contig_586;
 contig_300	contig_300;
-contig_586	contig_586;

Output output_kaks:  different than expected, difference (using diff):
( /tmp/tmp_uk_t_ojoutput1.tabular v. /tmp/tmpavmaputmoutput1.tabular )
--- local_file
+++ history_data
@@ -1,4 +1,4 @@
 SEQ1	SEQ2	Ka	Ks	Ka\Ks
-contig_241;	contig_241	1.5312	7.1619	0.2138
+contig_241	contig_241;	1.5312	7.1619	0.2138
+contig_586	contig_586;	1.7791	1.1181	1.5912
 contig_300	contig_300;	0.8653	3.7872	0.2285
-contig_586	contig_586;	1.7791	1.1181	1.5912

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
comparison_cond	`{"__current_case__": 0, "comparison": "paralogs"}`
options_type	`{"__current_case__": 0, "options_type_selector": "basic"}`
non_commercial_use	`"true"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-07-15T20:55:20Z

Hum, error is not the same as reported by a user. But it wasn't in a bug report, just an email. Rerunning again.

jennaj · 2022-07-15T20:55:25Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0

mvdbeek · 2022-07-15T20:59:44Z

Results (powered by Planemo)

Summary

State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis (Test tool test #1)

Problems:

Output output_species1_paralog:  different than expected, difference (using contains):
( /tmp/tmp47kjt3e4output_blastn_results1.tabular v. /tmp/tmp143obxehoutput_blastn_results1.tabular )
Failed to find 'contig_1;	contig_1;	100.00	346	0	0	1	346	1	346	0.0	640' in history data. (lines_diff=0).

Output output_rbhb_paralog:  different than expected, difference (using diff):
( /tmp/tmp59exbpc8output_paralogous_pairs.tabular v. /tmp/tmp3fzt2e0woutput_paralogous_pairs.tabular )
--- local_file
+++ history_data
@@ -1,3 +1,3 @@
-contig_241;	contig_241
 contig_300	contig_300;
 contig_586	contig_586;
+contig_241;	contig_241

Output output_kaks:  different than expected, difference (using diff):
( /tmp/tmprlkkm6hboutput1.tabular v. /tmp/tmpd3xz9m12output1.tabular )
--- local_file
+++ history_data
@@ -1,4 +1,4 @@
 SEQ1	SEQ2	Ka	Ks	Ka\Ks
-contig_241;	contig_241	1.5312	7.1619	0.2138
 contig_300	contig_300;	0.8653	3.7872	0.2285
 contig_586	contig_586;	1.7791	1.1181	1.5912
+contig_241;	contig_241	1.6082	3.1567	0.5095

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
comparison_cond	`{"__current_case__": 0, "comparison": "paralogs"}`
options_type	`{"__current_case__": 0, "options_type_selector": "basic"}`
non_commercial_use	`"true"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-07-26T19:15:54Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0

mvdbeek · 2022-07-26T19:18:22Z

Results (powered by Planemo)

Summary

State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis (Test tool test #1)

Problems:

Output output_species1_paralog:  different than expected, difference (using contains):
( /tmp/tmpyjqjpf1foutput_blastn_results1.tabular v. /tmp/tmpb7yhvuv7output_blastn_results1.tabular )
Failed to find 'contig_1;	contig_1;	100.00	346	0	0	1	346	1	346	0.0	640' in history data. (lines_diff=0).

Output output_rbhb_paralog:  different than expected, difference (using diff):
( /tmp/tmpmx1vdcwsoutput_paralogous_pairs.tabular v. /tmp/tmpm9xvm7qwoutput_paralogous_pairs.tabular )
--- local_file
+++ history_data
@@ -1,3 +1,3 @@
-contig_241;	contig_241
+contig_241	contig_241;
 contig_300	contig_300;
-contig_586	contig_586;
+contig_586;	contig_586

Output output_kaks:  different than expected, difference (using diff):
( /tmp/tmpe39vlnpaoutput1.tabular v. /tmp/tmpqi6ufj0loutput1.tabular )
--- local_file
+++ history_data
@@ -1,4 +1,4 @@
 SEQ1	SEQ2	Ka	Ks	Ka\Ks
-contig_241;	contig_241	1.5312	7.1619	0.2138
+contig_241	contig_241;	1.5312	7.1619	0.2138
 contig_300	contig_300;	0.8653	3.7872	0.2285
-contig_586	contig_586;	1.7791	1.1181	1.5912
+contig_586;	contig_586	1.7791	1.1181	1.5912

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
comparison_cond	`{"__current_case__": 0, "comparison": "paralogs"}`
options_type	`{"__current_case__": 0, "options_type_selector": "basic"}`
non_commercial_use	`"true"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2022-07-26T20:06:34Z

The tool is missing a dependency when run at usegalaxy.org.

See dataset 13 -> https://usegalaxy.org/u/jen-galaxyproject/h/test-kaksanalysis-ksdistribution

This superficially looks related: jemalloc/jemalloc#1327

Running on user test data results in green successful outputs that contain this content -- a log message from the tool instead of tool output. This should fail the tool.

Tue Jul 26 19:43:12 2022 - Starting nonsynonymous (ka) and synonymous (ks) analysis
Tue Jul 26 19:43:15 2022 - Determining orthologous pairs using reciprocal best BLAST
Tue Jul 26 19:43:17 2022 - Determining orthologous pairs using conditional reciprocal best BLAST
/usr/local/bin/ruby: error while loading shared libraries: libjemalloc.so.1: cannot open shared object file: No such file or directory
-- Tue Jul 26 19:43:18 2022 - Running CRB-BLAST failed

Happens at these clusters:

Compute Resource | Galaxy cluster
Compute Resource | Jetstream (first available zone)
Compute Resource | TACC Stampede 2 normal (KNL) partition
Compute Resource | [TESTING/DEVELOPMENT] Galaxy cluster

Still queued at these
Compute Resource | TACC Stampede 2 SKX partition
Compute Resource | TACC Stampede 2 normal (KNL) partition

jennaj · 2023-06-12T23:30:56Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0

jennaj · 2023-06-12T23:35:18Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.3.0

mvdbeek · 2023-06-12T23:36:52Z

Results (powered by Planemo)

Summary

State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis (Test tool test #1)

Problems:

Output output_species1_paralog:  different than expected, difference (using contains):
( /tmp/tmpfq1yietkoutput_blastn_results1.tabular v. /tmp/tmpy01hvjgqoutput_blastn_results1.tabular )
Failed to find 'contig_1;	contig_1;	100.00	346	0	0	1	346	1	346	0.0	640' in history data. (lines_diff=0).

Output output_kaks:  different than expected, difference (using diff):
( /tmp/tmpzq14ejepoutput1.tabular v. /tmp/tmp6t8zaw1houtput1.tabular )
--- local_file
+++ history_data
@@ -1,4 +1,4 @@
 SEQ1	SEQ2	Ka	Ks	Ka\Ks
 contig_241;	contig_241	1.5312	7.1619	0.2138
-contig_300	contig_300;	0.8653	3.7872	0.2285
-contig_586	contig_586;	1.7791	1.1181	1.5912
+contig_300	contig_300;	2.6654	2.0520	1.2989
+contig_586	contig_586;	1.6212	0.8171	1.9841

Command Line:

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
comparison_cond	`{"__current_case__": 0, "comparison": "paralogs"}`
options_type	`{"__current_case__": 0, "options_type_selector": "basic"}`
non_commercial_use	`true`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

mvdbeek · 2023-06-12T23:38:26Z

Results (powered by Planemo)

Summary

State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis (Test tool test #1)

Problems:

Output output_species1_paralog:  different than expected, difference (using contains):
( /tmp/tmpmnze0z59output_blastn_results1.tabular v. /tmp/tmpk4w7za8ioutput_blastn_results1.tabular )
Failed to find 'contig_1;	contig_1;	100.00	346	0	0	1	346	1	346	0.0	640' in history data. (lines_diff=0).

Output output_rbhb_paralog:  different than expected, difference (using diff):
( /tmp/tmpcd2l8b6voutput_paralogous_pairs.tabular v. /tmp/tmpr_yfxp95output_paralogous_pairs.tabular )
--- local_file
+++ history_data
@@ -1,3 +1,3 @@
-contig_241;	contig_241
 contig_300	contig_300;
-contig_586	contig_586;
+contig_241	contig_241;
+contig_586;	contig_586

Output output_kaks:  different than expected, difference (using diff):
( /tmp/tmp3yjo9ft0output1.tabular v. /tmp/tmpx5xmlwu3output1.tabular )
--- local_file
+++ history_data
@@ -1,4 +1,4 @@
 SEQ1	SEQ2	Ka	Ks	Ka\Ks
-contig_241;	contig_241	1.5312	7.1619	0.2138
-contig_300	contig_300;	0.8653	3.7872	0.2285
-contig_586	contig_586;	1.7791	1.1181	1.5912
+contig_300	contig_300;	2.6654	2.0520	1.2989
+contig_241	contig_241;	1.5312	7.1619	0.2138
+contig_586;	contig_586	1.6212	0.8171	1.9841

Command Line:

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
comparison_cond	`{"__current_case__": 0, "comparison": "paralogs"}`
options_type	`{"__current_case__": 0, "options_type_selector": "basic"}`
non_commercial_use	`true`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj · 2023-06-17T00:11:44Z

~~Todo: jen, retest across current clusters~~ tool updated, testing that

jennaj · 2023-06-17T00:12:26Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis/1.0.4.0

mvdbeek · 2023-06-17T00:14:24Z

Results (powered by Planemo)

Summary

State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/greg/plant_tribes_kaks_analysis/plant_tribes_kaks_analysis (Test tool test #1)

Problems:

Output output_species1_paralog:  different than expected, difference (using contains):
( /tmp/tmpjlxeetsgoutput_blastn_results1.tabular v. /tmp/tmpfp4scq23output_blastn_results1.tabular )
Failed to find 'contig_1;	contig_1;	100.00	346	0	0	1	346	1	346	0.0	640' in history data. (lines_diff=0).

Output output_rbhb_paralog:  different than expected, difference (using diff):
( /tmp/tmpq6bz_w_2output_paralogous_pairs.tabular v. /tmp/tmppdripzfcoutput_paralogous_pairs.tabular )
--- local_file
+++ history_data
@@ -1,3 +1,3 @@
-contig_241;	contig_241
-contig_300	contig_300;
-contig_586	contig_586;
+contig_300;	contig_300
+contig_241	contig_241;
+contig_586;	contig_586

Output output_kaks:  different than expected, difference (using diff):
( /tmp/tmpgce2bqxtoutput1.tabular v. /tmp/tmp5_r2dya7output1.tabular )
--- local_file
+++ history_data
@@ -1,4 +1,4 @@
 SEQ1	SEQ2	Ka	Ks	Ka\Ks
-contig_241;	contig_241	1.5312	7.1619	0.2138
-contig_300	contig_300;	0.8653	3.7872	0.2285
-contig_586	contig_586;	1.7791	1.1181	1.5912
+contig_300;	contig_300	2.6654	2.0520	1.2989
+contig_241	contig_241;	1.5312	7.1619	0.2138
+contig_586;	contig_586	1.6212	0.8171	1.9841

Command Line:

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
comparison_cond	`{"__current_case__": 0, "comparison": "paralogs"}`
options_type	`{"__current_case__": 0, "options_type_selector": "basic"}`
non_commercial_use	`true`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"fasta"`

jennaj mentioned this issue Jul 26, 2022

test ks_distribution 1.0.3.0 #51

Closed

jennaj mentioned this issue Jul 26, 2022

Fix dependency for plant_tribes_kaks_analysis 1.0.3.0 galaxyproject/usegalaxy-tools#535

Closed

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test plant_tribes_kaks_analysis 1.0.3.0 #49

test plant_tribes_kaks_analysis 1.0.3.0 #49

jennaj commented Jul 15, 2022

jennaj commented Jul 15, 2022

mvdbeek commented Jul 15, 2022

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mvdbeek commented Jul 26, 2022

jennaj commented Jul 26, 2022 •

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jennaj commented Jun 12, 2023

jennaj commented Jun 12, 2023

mvdbeek commented Jun 12, 2023

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jennaj commented Jun 17, 2023 •

edited

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jennaj commented Jun 17, 2023

mvdbeek commented Jun 17, 2023

test plant_tribes_kaks_analysis 1.0.3.0 #49

test plant_tribes_kaks_analysis 1.0.3.0 #49

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jennaj commented Jul 15, 2022

jennaj commented Jul 15, 2022

mvdbeek commented Jul 15, 2022

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jennaj commented Jul 15, 2022

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