Crux comet does not write output files to the --output-dir

[Brian Connolly]

With the latest release of Crux (3.2.fb7f902) the comet output files (pep.xml, pin, etc) are no longer written to the directory specified by the --output-dir command line option. 

Here is an example of what is happening: 

Starting file structure 

ls -la
-rw-r--r--@  1 bconn  staff   5394979 Sep  4 13:09 2020_0212_Loomis_22_DDA_SIM60_400_35.mzML
-rw-r--r--   1 bconn  staff   8673876 Nov 12 08:10 2020_0212_Loomis_23_DDA_SIM60_515_35.mzML
-rw-r--r--@  1 bconn  staff  13905094 Sep  4 13:12 Human_PD_ClinVarpep.fasta
drwxr-xr-x  11 bconn  staff       352 Nov 13 08:11 crux_output
-rw-r--r--   1 bconn  staff      1342 Nov 12 08:10 crux_params_file.template
drwxr-xr-x   2 bconn  staff        64 Nov 13 08:03 run

Using v3.2 (release version), the following commands were run

cd run
/crux comet --parameter-file ../crux_params_file.template ../2020_0212_Loomis_22_DDA_SIM60_400_35.mzML ../2020_0212_Loomis_23_DDA_SIM60_515_35.mzML ../Human_PD_ClinVarpep.fasta --output-dir ../crux_output

the results are written to the directory specified in the --output-dir command line option

ls -la ../crux_output/
-rw-r--r--  1 root root 1246927 Nov 13 16:11 comet.2020_0212_Loomis_22_DDA_SIM60_400_35.target.pep.xml
-rw-r--r--  1 root root  457603 Nov 13 16:11 comet.2020_0212_Loomis_22_DDA_SIM60_400_35.target.pin
-rw-r--r--  1 root root  255246 Nov 13 16:11 comet.2020_0212_Loomis_22_DDA_SIM60_400_35.target.txt
-rw-r--r--  1 root root 1803653 Nov 13 16:11 comet.2020_0212_Loomis_23_DDA_SIM60_515_35.target.pep.xml
-rw-r--r--  1 root root  667940 Nov 13 16:11 comet.2020_0212_Loomis_23_DDA_SIM60_515_35.target.pin
-rw-r--r--  1 root root  386304 Nov 13 16:11 comet.2020_0212_Loomis_23_DDA_SIM60_515_35.target.txt
-rw-r--r--  1 root root    2647 Nov 13 16:11 comet.log.txt
-rw-r--r--  1 root root   72090 Nov 13 16:11 comet.params.txt

When running the same command with v3.2.fb7f902 the contents are the crux-output directory are 

ls -la ../crux_output/
-rw-r--r--  1 root root  1649 Nov 13 16:05 comet.log.txt
-rw-r--r--  1 root root 93654 Nov 13 16:05 comet.params.txt

And the other output files are written to the directory which hold the mzML files 

ls -la ../
-rw-r--r--  1 root root  5394979 Sep  4 20:09 2020_0212_Loomis_22_DDA_SIM60_400_35.mzML
-rw-r--r--  1 root root   426112 Nov 13 16:05 2020_0212_Loomis_22_DDA_SIM60_400_35.pin
-rw-r--r--  1 root root  1245190 Nov 13 16:05 2020_0212_Loomis_22_DDA_SIM60_400_35.target.pep.xml
-rw-r--r--  1 root root   255246 Nov 13 16:05 2020_0212_Loomis_22_DDA_SIM60_400_35.target.txt
-rw-r--r--  1 root root  8673876 Nov 12 16:10 2020_0212_Loomis_23_DDA_SIM60_515_35.mzML
-rw-r--r--  1 root root   623210 Nov 13 16:05 2020_0212_Loomis_23_DDA_SIM60_515_35.pin
-rw-r--r--  1 root root  1801034 Nov 13 16:05 2020_0212_Loomis_23_DDA_SIM60_515_35.target.pep.xml
-rw-r--r--  1 root root   386304 Nov 13 16:05 2020_0212_Loomis_23_DDA_SIM60_515_35.target.txt
-rw-r--r--  1 root root 13905094 Sep  4 20:12 Human_PD_ClinVarpep.fasta
drwxr-xr-x  5 root root      160 Nov 13 16:05 crux_output
-rw-r--r--  1 root root     1342 Nov 12 16:10 crux_params_file.template
drwxr-xr-x  2 root root       64 Nov 13 16:03 run

I have attached the params file which I am using in this test.  Thank you for your help. 

Brian Connolly 

[William S Noble]

Sorry to hear this, and thanks for letting us know. We will look into it and get back to you soon.

Bill

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[Charles E Grant]

Hi Brian,

I haven’t been able to reproduce this problem so far. Could you let us know what platform you are working on? You mentioned attaching the parameter file you used, but no file was attached. Could  you forward that file to us?  If you still have it, it would also be helpful if you could forward the file crux_output/comet.log.txt.

Thanks!

Charles

[Brian Connolly]

Please find attached the params file that was used.

Brian

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