singularity issue when run adap

[ammorse]

Running the container with singularity on the test data after modifying the parameter.txt file for ADAP results in errors on both a linux workstation and a computing cluster - see attached adap.log file. The only modifications done to the parameter file were 1) change line 143 from "false" to "true" and 2) change line 178 from "openMS" to "ADAP".

The test data runs fine without modification to the parameter.txt file on the linux workstation and the cluster.

Any suggestions would be appreciated!

Alison

adap.log

[adelabriere]

Hi @ammorse thanks for reporting your problem

There is a problem with the number of cores detected by SLAW here:

2022-01-10|14:49:01|INFO: Total memory available: 374760 and 72 cores. The workflow will use 5278 Mb by core on 1 cores.

SLAW use N-1 cores for optimization, in this case as there is 1 it is 0. I'll add an error message for that.

I am not sure exactly why but you can pass the number of cores that you use like this by passing the NCORES environment variables ie:

SINGULARITYENV_NCORES=10

It should solve the problem. If it does not or you find an exaplanation at why SLAW detect only 1 core please let me known.

[ammorse]

Thanks for the quick response!

I increased the cores to 12 but get the same error:

2022-01-10|15:34:49|INFO: Total memory available: 374100 and 72 cores. The workflow will use 5269 Mb by core on 12 cores. 2022-01-10|15:34:49|INFO: Guessing polarity from file:DDA1.mzML 2022-01-10|15:34:49|DEBUG: Rscript /pylcmsprocessing/Rscript/get_polarity.R "/input/DDA1.mzML" "/output/polarity" 2022-01-10|15:34:51|INFO: Polarity detected: positive 2022-01-10|15:34:51|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-10|15:34:51|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-10|15:34:52|INFO: STEP: initialisation TOTAL_TIME:2.61s LAST_STEP:2.61s 2022-01-10|15:34:52|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-10|15:34:52|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-10|15:34:53|INFO: Building input 2022-01-10|15:34:53|INFO: Computing MZmine parameters 2022-01-10|15:34:54|INFO: 4 existing peak picking 0 added. 2022-01-10|15:34:54|INFO: Building softwares 2022-01-10|15:34:54|INFO: Building peakpicking 2022-01-10|15:34:54|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_1_8724ba244b72587de8964b2845313a95.xml" 2022-01-10|15:34:54|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_2_ab56e050d8986b8f2c15ddd9de546b0a.xml" 2022-01-10|15:34:54|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_3_c9437a898051dd8ae8d7c7e3028deecd.xml" 2022-01-10|15:34:54|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_4_c5cfe1da97cf769434a67fb9d32a0002.xml" 2022-01-10|15:34:54|DEBUG: stderr:/bin/sh: 1: /MZmine-2.52-Linux/startMZmine-Linux: Permission denied

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Monday, January 10, 2022 3:33 PM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Hi @ammorsehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ammorse&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=eDc5CrCDOx5No3uIJSqts6dJnlx2uUeOftjvufg5nFHB2tXXAngDoOP7b9J_zQsC&s=VjmLNU721qZ5QHo6QLrMgUyqSUxeG8rM7EKaOunBj7c&e= thanks for reporting your problem

There is a problem with the number of cores detected by SLAW here:

2022-01-10|14:49:01|INFO: Total memory available: 374760 and 72 cores. The workflow will use 5278 Mb by core on 1 cores.

SLAW use N-1 cores for optimization, in this case as there is 1 it is 0. I'll add an error message for that.

I am not sure exactly why but you can pass the number of cores that you use like this by passing the NCORES environment variables ie:

SINGULARITYENV_NCORES=10

It should solve the problem. If it does not or you find an exaplanation at why SLAW detect only 1 core please let me known.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1009318092&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=eDc5CrCDOx5No3uIJSqts6dJnlx2uUeOftjvufg5nFHB2tXXAngDoOP7b9J_zQsC&s=9zRYKEiX63J0iCWSf0eJuIJcyuzkfk6vRHMSzHtxf_Y&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWCZYBDQOEWTALB6GYODUVM673ANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=eDc5CrCDOx5No3uIJSqts6dJnlx2uUeOftjvufg5nFHB2tXXAngDoOP7b9J_zQsC&s=DMl9ZXOezF9osrfbpnZOXaIkw_XrvM14oF92hlmsqjo&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=eDc5CrCDOx5No3uIJSqts6dJnlx2uUeOftjvufg5nFHB2tXXAngDoOP7b9J_zQsC&s=I84Oh5L-weauuiSpNe8SsSBqX9Kyv4dXnEpZf5-1OTM&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=eDc5CrCDOx5No3uIJSqts6dJnlx2uUeOftjvufg5nFHB2tXXAngDoOP7b9J_zQsC&s=opIl6tUqnJnZPq-K_65OX8y_zGHfI-wBxWM4oWa9u3M&e=. You are receiving this because you were mentioned.Message ID: @.***>

[adelabriere]

Sorry I looked at your issue fast and only focused on the last error.

I just retested the adelabriere/slaw:latest with ADAP optimization with singularity on my laptop and on our cluster and both worked as intended. ADAP may be the trickiest to run as MZmine is writing some temporary files internally. Here the command that I used to run the container:

SINGULARITYENV_LOGGING=DEBUG SINGULARITYENV_MEMORY=XXXX SINGULARITYENV_NCORES=X singularity run -C -W work_dir -B your_input:/input -B your_output:/output docker://adelabriere/slaw:latest

-W work_dir needs to be a writable folder. I think that may be the cause of your problem. -C is also required on our cluster.

The version of singularity that I used is singularity 3.6.1

Maybe adding these options will solve you problem ?

[ammorse]

Hi Alexis,

I'm still having issues running slaw with adap on your test data. Getting the same error on my linux workstation and on a mac - see below. Any suggestions?

Thanks! Alison

INFO: Using cached SIF image 2022-01-13|09:21:56|INFO: Total memory available: 379454 and 72 cores. The workflow will use 5269 Mb by core on 12 cores. 2022-01-13|09:21:56|INFO: Guessing polarity from file:DDA1.mzML 2022-01-13|09:21:56|DEBUG: Rscript /pylcmsprocessing/Rscript/get_polarity.R "/input/DDA1.mzML" "/output/polarity" 2022-01-13|09:22:02|INFO: Polarity detected: positive 2022-01-13|09:22:02|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-13|09:22:02|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-13|09:22:04|INFO: STEP: initialisation TOTAL_TIME:8.22s LAST_STEP:8.22s 2022-01-13|09:22:05|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-13|09:22:05|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-13|09:22:05|INFO: Building input 2022-01-13|09:22:05|INFO: Computing MZmine parameters 2022-01-13|09:22:07|INFO: 4 existing peak picking 0 added. 2022-01-13|09:22:07|INFO: Building softwares 2022-01-13|09:22:07|INFO: Building peakpicking 2022-01-13|09:22:07|INFO: Peak picking finished 0 files not processed on a total of 0 2022-01-13|09:22:07|INFO: No corrections to do 2022-01-13|09:22:07|DEBUG: Rscript /pylcmsprocessing/Rscript/extractingMGFfromMZML.R "/output/temp_processing_db.sqlite" "/output/ADAP/msms" 0.0 71 True 2022-01-13|09:22:07|DEBUG: stdout:Extracting all MS-MS spectra. 2022-01-13|09:22:07|DEBUG: stderr:Linking to: OpenSSL 1.1.1f 31 Mar 2020 MS-MS spectra extraction finished 2022-01-13|09:22:07|INFO: MS2 extraction finished 2022-01-13|09:22:07|INFO: Starting peaktable filtration Traceback (most recent call last): File "/wrapper_docker.py", line 223, in exp.filter_peaktables(filtering_string) File "/pylcmsprocessing/model/experiment.py", line 673, in filter_peaktables with multiprocessing.Pool(min(num_workers, len(all_peaktables))) as executor: File "/usr/lib/python3.8/multiprocessing/context.py", line 119, in Pool return Pool(processes, initializer, initargs, maxtasksperchild, File "/usr/lib/python3.8/multiprocessing/pool.py", line 205, in init raise ValueError("Number of processes must be at least 1") ValueError: Number of processes must be at least 1

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Monday, January 10, 2022 4:12 PM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Sorry I looked at your issue fast and only focused on the last error.

I just retested the adelabriere/slaw:latest with ADAP optimization with singularity on my laptop and on our cluster and both worked as intended. ADAP may be the trickiest to run as MZmine is writing some temporary files internally. Here the command that I used to run the container:

SINGULARITYENV_LOGGING=DEBUG SINGULARITYENV_MEMORY=XXXX SINGULARITYENV_NCORES=X singularity run -C -W work_dir -B your_input:/input -B your_output:/output docker://adelabriere/slaw:latest

-W work_dir needs to be a writable folder. I think that may be the cause of your problem. -C is also required on our cluster.

The version of singularity that I used is singularity 3.6.1

Maybe adding these options will solve you problem ?

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1009347431&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=fcdSv1Ivi_MqHV25uD51q7bqBsVyerqQFZYuV83RssnqEsRMib5Nf6_hEUXKxYzI&s=P6OV9q3xC3t7E_f8DQEjowHcr7NQHEBfmXqzdBurlVg&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC5GVBHMG5VUUA2IWPDUVNDURANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=fcdSv1Ivi_MqHV25uD51q7bqBsVyerqQFZYuV83RssnqEsRMib5Nf6_hEUXKxYzI&s=aUzbm4l53yzaj9xZOUZrePvJDfdEJRVS8pZRRGuC1zA&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=fcdSv1Ivi_MqHV25uD51q7bqBsVyerqQFZYuV83RssnqEsRMib5Nf6_hEUXKxYzI&s=PeVTxuZrJG9G35IC_ZM_NTyiYHweTiC82VIrZ14QLi4&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=fcdSv1Ivi_MqHV25uD51q7bqBsVyerqQFZYuV83RssnqEsRMib5Nf6_hEUXKxYzI&s=492a_wQrp3QAgqDKxaQuqRORBFcMLb3u5km2HMBUZVg&e=. You are receiving this because you were mentioned.Message ID: @.***>

[adelabriere]

Hi @ammorse, sorry to hear that. Thanks to you I just fixed this bug in e01577b48bdb8692df6a81a2462e619609c5300d. It was only happening if a processing was restarted with all the peaktables correctly computed. To finish the processing:

1. Remove the ADAP folder and restart.
2. Wait 10 minutes and use adelabriere/slaw:dev, I am running some test but I should integrate the change to adelabriere/slaw:latest this evening. So normally you could also just use adelabriere/slaw:latest tomorrow.

I hope it fixes your issues.

[ammorse]

Thanks Alexis!

Will try in a bit 🙂

Alison

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Thursday, January 13, 2022 9:42 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Hi, sorry to hear that. Thanks to you I just fixed this bug in e01577bhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_commit_e01577b48bdb8692df6a81a2462e619609c5300d&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=9IyerhWYIEs4m1b8NM8XmKkqdOAePnhpRd9xWN95L24&e=. To finish the processing:

1. Remove the ADAP folder and restart.
2. Wait 10 minutes and use adelabriere/slaw:dev, I am running some test but I should integrate the change to adelabriere/slaw:latest this evening. So normally you could also just use adelabriere/slaw:latest tomorrow.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1012199475&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=s7U__pyzGi7Fis6BAaFQllY7KLIiS1hyDtde4DCJmls&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC4XQDOY3KN7VUOT24TUV3QF7ANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=juTRLkgJNQrG_3qtMjLLolww-IQXrQUBw37VQodiDT4&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=pFO-8y3x0PzMSIXTGUBurw-TDvusjX-BXj_eqb2m2As&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=-kp6F0bgzamh2IUUy460msWLQhIz5Tr9q6hx7H5YHRE&e=. You are receiving this because you were mentioned.Message ID: @.***>

[ammorse]

Hi Alexis,

running with docker://adelabriere/slaw:dev I get the following error

INFO: Using cached SIF image Traceback (most recent call last): File "/wrapper_docker.py", line 13, in from pylcmsprocessing.model.helper.UI import UI File "/pylcmsprocessing/init.py", line 2, in import model.experiment File "/pylcmsprocessing/model/experiment.py", line 674 if min_process>0: ^ SyntaxError: invalid syntax

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Thursday, January 13, 2022 9:53 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

Thanks Alexis!

Will try in a bit 🙂

Alison

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Thursday, January 13, 2022 9:42 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Hi, sorry to hear that. Thanks to you I just fixed this bug in e01577bhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_commit_e01577b48bdb8692df6a81a2462e619609c5300d&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=9IyerhWYIEs4m1b8NM8XmKkqdOAePnhpRd9xWN95L24&e=. To finish the processing:

1. Remove the ADAP folder and restart.
2. Wait 10 minutes and use adelabriere/slaw:dev, I am running some test but I should integrate the change to adelabriere/slaw:latest this evening. So normally you could also just use adelabriere/slaw:latest tomorrow.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1012199475&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=s7U__pyzGi7Fis6BAaFQllY7KLIiS1hyDtde4DCJmls&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC4XQDOY3KN7VUOT24TUV3QF7ANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=juTRLkgJNQrG_3qtMjLLolww-IQXrQUBw37VQodiDT4&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=pFO-8y3x0PzMSIXTGUBurw-TDvusjX-BXj_eqb2m2As&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=-kp6F0bgzamh2IUUy460msWLQhIz5Tr9q6hx7H5YHRE&e=. You are receiving this because you were mentioned.Message ID: @.***>

[ammorse]

Hi Alexis,

Thanks for the help! I pulled and reran your test data (docker://adelabriere/slaw:latest) using adap and height. I think all is good but I am seeing some stderr/Error - see attached file (testData_adap.log).

Alison

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Thursday, January 13, 2022 11:27 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

Hi Alexis,

running with docker://adelabriere/slaw:dev I get the following error

INFO: Using cached SIF image Traceback (most recent call last): File "/wrapper_docker.py", line 13, in from pylcmsprocessing.model.helper.UI import UI File "/pylcmsprocessing/init.py", line 2, in import model.experiment File "/pylcmsprocessing/model/experiment.py", line 674 if min_process>0: ^ SyntaxError: invalid syntax

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Thursday, January 13, 2022 9:53 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

Thanks Alexis!

Will try in a bit 🙂

Alison

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Thursday, January 13, 2022 9:42 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Hi, sorry to hear that. Thanks to you I just fixed this bug in e01577bhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_commit_e01577b48bdb8692df6a81a2462e619609c5300d&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=9IyerhWYIEs4m1b8NM8XmKkqdOAePnhpRd9xWN95L24&e=. To finish the processing:

1. Remove the ADAP folder and restart.
2. Wait 10 minutes and use adelabriere/slaw:dev, I am running some test but I should integrate the change to adelabriere/slaw:latest this evening. So normally you could also just use adelabriere/slaw:latest tomorrow.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1012199475&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=s7U__pyzGi7Fis6BAaFQllY7KLIiS1hyDtde4DCJmls&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC4XQDOY3KN7VUOT24TUV3QF7ANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=juTRLkgJNQrG_3qtMjLLolww-IQXrQUBw37VQodiDT4&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=pFO-8y3x0PzMSIXTGUBurw-TDvusjX-BXj_eqb2m2As&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=z9JNoR2BeFRG-TQpo4VSMNWpFuE-CGUBi9O6hGT3ZDedZfJvb6ZtOLLNyJnlquBw&s=-kp6F0bgzamh2IUUy460msWLQhIz5Tr9q6hx7H5YHRE&e=. You are receiving this because you were mentioned.Message ID: @.***>

[adelabriere]

Hi Alison, I don t see the attached file ? I can confirm however that there is an ADAP issue which was not there before, and I have a clear idea of its origin. I ll tag you here when everything is fixed and both singularity and docker run fine with ADAP. Sorry for the lost time.

[adelabriere]

@ammorse The permission problem is fixed for both latest and dev and I was able to fully process the ADAP examples with both singularity and docker. I tried to setup some automated building but it was messing up the permission of MZmine. I hope it solves your last issue if it does not please paste the log.

[ammorse]

Thanks Alexis!

I'll pull and give it a go.

Alison

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Friday, January 14, 2022 5:52 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

@ammorsehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ammorse&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=0mSe3PVGTUOfOivTrkn30J9k9nAMVAnfP8ms-vNpTlc&e= The permission problem is fixed for both latest and dev and I was able to fully process the ADAP examples with both singularity and docker. I tried to setup some automated building but it was messing up the permission of MZmine. I hope it solves your last issue.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1013013813&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=78fgXo0JSvBYmoDgtW51seyJ3td0y07O5Na62L2jG-8&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC5RURKG4QE6J5I4ROLUV755XANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=TC6nal2iJ9o0iwwfX8Kej2OzUOD3t1CBh-yrZHaJqLY&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=eYqyaoAr0E1VjIG9lhFBTcclqb8qfeG7ctdicOn8UJI&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=Cv1O4Y0je6tqCy_6BfTsaj8tqi03h_eTWICx0Mmskjs&e=. You are receiving this because you were mentioned.Message ID: @.***>

[ammorse]

Ran with adap on your testdata after pulling and got the following error:

INFO: Using cached SIF image 2022-01-14|10:08:58|INFO: Total memory available: 376777 and 72 cores. The workflow will use 5269 Mb by core on 12 cores. 2022-01-14|10:08:58|INFO: Guessing polarity from file:DDA1.mzML 2022-01-14|10:08:58|DEBUG: Rscript /pylcmsprocessing/Rscript/get_polarity.R "/input/DDA1.mzML" "/output/polarity" 2022-01-14|10:09:00|INFO: Polarity detected: positive 2022-01-14|10:09:00|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:09:00|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:09:00|INFO: STEP: initialisation TOTAL_TIME:1.98s LAST_STEP:1.98s 2022-01-14|10:09:01|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:09:01|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:09:01|INFO: Building input 2022-01-14|10:09:01|INFO: Computing MZmine parameters 2022-01-14|10:09:02|INFO: 4 existing peak picking 0 added. 2022-01-14|10:09:02|INFO: Building softwares 2022-01-14|10:09:02|INFO: Building peakpicking 2022-01-14|10:09:02|INFO: Peak picking finished 0 files not processed on a total of 0 2022-01-14|10:09:02|INFO: No corrections to do 2022-01-14|10:09:02|DEBUG: Rscript /pylcmsprocessing/Rscript/extractingMGFfromMZML.R "/output/temp_processing_db.sqlite" "/output/ADAP/msms" 0.0 12 True 2022-01-14|10:09:06|DEBUG: stdout:Extracting all MS-MS spectra. 2022-01-14|10:09:06|DEBUG: stderr:Linking to: OpenSSL 1.1.1f 31 Mar 2020 MS-MS spectra extraction finished 2022-01-14|10:09:06|INFO: MS2 extraction finished 2022-01-14|10:09:06|INFO: Starting peaktable filtration 2022-01-14|10:09:06|INFO: Done peaktables filtration 2022-01-14|10:09:06|INFO: STEP: peakpicking TOTAL_TIME:7.87s LAST_STEP:5.90s 2022-01-14|10:09:06|INFO: Alignment finished 2022-01-14|10:09:06|INFO: STEP: alignment TOTAL_TIME:7.88s LAST_STEP:0.00s 2022-01-14|10:09:06|DEBUG: Rscript /pylcmsprocessing/Rscript/gap_filling_refactored.R "/output/temp_processing_db.sqlite" "/output/datamatrices/datamatrix_50660bda0ce5a823e93a7cc9474963f6.csv" > 2022-01-14|10:09:17|DEBUG: stdout:<simpleError in mapply(FUN = FUN, ..., MoreArgs = MoreArgs, SIMPLIFY = SIMPLIFY): zero-length inputs cannot be mixed with those of non-zero length> NULL 2022-01-14|10:09:17|DEBUG: stderr:Create profile matrix with method 'bin' and step 1 ... OK Error in h5read(hdf5_file, path_infer) : Object 'FEATURES/MFEAT1_1' does not exist in this HDF5 file. Calls: extractMissingInformationsAllBatches ... eval -> eval -> eval -> mapply -> -> h5read Execution halted 2022-01-14|10:09:17|INFO: Gap filling and isotopic pattern extraction finished. 2022-01-14|10:09:17|INFO: STEP: gap-filling TOTAL_TIME:18.81s LAST_STEP:10.94s 2022-01-14|10:09:17|INFO: Annotation finished 2022-01-14|10:09:17|INFO: STEP: annotation TOTAL_TIME:18.82s LAST_STEP:0.00s 2022-01-14|10:09:17|INFO: Processing finished.

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Friday, January 14, 2022 9:22 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

Thanks Alexis!

I'll pull and give it a go.

Alison

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Friday, January 14, 2022 5:52 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

@ammorsehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ammorse&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=0mSe3PVGTUOfOivTrkn30J9k9nAMVAnfP8ms-vNpTlc&e= The permission problem is fixed for both latest and dev and I was able to fully process the ADAP examples with both singularity and docker. I tried to setup some automated building but it was messing up the permission of MZmine. I hope it solves your last issue.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1013013813&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=78fgXo0JSvBYmoDgtW51seyJ3td0y07O5Na62L2jG-8&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC5RURKG4QE6J5I4ROLUV755XANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=TC6nal2iJ9o0iwwfX8Kej2OzUOD3t1CBh-yrZHaJqLY&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=eYqyaoAr0E1VjIG9lhFBTcclqb8qfeG7ctdicOn8UJI&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=nGXlNqJKAiKVgGIv0SJmESXDVBIgkV1dS6oFPrwbaEo8YHBdiQMuyjwOeJWqL2q0&s=Cv1O4Y0je6tqCy_6BfTsaj8tqi03h_eTWICx0Mmskjs&e=. You are receiving this because you were mentioned.Message ID: @.***>

[adelabriere]

Could you clean the output folder and retry just letting the parameters.txt file, it seems like you have artifact from an old processing. I think it should solve this.

[ammorse]

my bad! cleaned output dir and reran with test data and adap - got output! going to try with a subset of our data next

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Friday, January 14, 2022 10:20 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Could you clean the output folder and retry just letting the parameters.txt file, it seems like you have artifact from an old processing. I think it should solve this.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1013217693&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=R76ZWJpJw0wZ3M73Opv4lN3OiQkaiJ38E1mxjuvL0mI&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC34KYPIJBF6JY7HL63UWA5LPANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=Gz-_aPcErVVUPngjtx5HOr5730yxPGJ2v0atI551_Ww&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=XYZ0TCuQXqa6TaxLskGG4oFeSplIH5yEi68JhjCnPIM&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=_7ewMiDRGqO0ICONO4zy-ytpamIYexf2UV4637WMRPg&e=. You are receiving this because you were mentioned.Message ID: @.***>

[ammorse]

with my data I'm getting a Java error:

INFO: Using cached SIF image 2022-01-14|10:59:53|INFO: Total memory available: 376406 and 72 cores. The workflow will use 4 Mb by core on 12 cores. 2022-01-14|10:59:53|INFO: Guessing polarity from file:b1_aos_129.mzML 2022-01-14|10:59:53|DEBUG: Rscript /pylcmsprocessing/Rscript/get_polarity.R "/input/b1_aos_129.mzML" "/output/polarity" 2022-01-14|10:59:55|INFO: Polarity detected: positive 2022-01-14|10:59:55|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:55|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:56|INFO: STEP: initialisation TOTAL_TIME:2.48s LAST_STEP:2.48s 2022-01-14|10:59:56|INFO: An ADAP batch file has been generated in the /output directory, you ca use it to refine peakpicking parameters using MZmine. 2022-01-14|10:59:56|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:56|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:57|INFO: Building input 2022-01-14|10:59:57|INFO: Computing MZmine parameters 2022-01-14|10:59:58|INFO: 0 existing peak picking 11 added. 2022-01-14|10:59:58|INFO: Building softwares 2022-01-14|10:59:58|INFO: Building peakpicking 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_1_e7ce7e8c6b7cb3d7d48fec2c7d71ebec.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_2_970dc76067207d1b924d080e643d84aa.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_3_4a617aa20e4f048f0cdc85d5559d7783.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_4_c96b35725531166fbfd80129e0080993.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_5_2eb6635caec00b3cd7344bc8f5cdac4f.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_6_d8eaa1acf475e1ceaa29dce505a2e374.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_7_08577539ac4063c4667e9f24375d02df.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_8_95f4493cd78798cb00428dd4c0301f9c.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_9_92d8c6e96856e8b1044ded7b67752030.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_10_2cb78523b3e947fcd9ae0c93e8bd7979.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_11_91ad051e8c2a9f4eb5fd74602a4b485c.xml" 2022-01-14|10:59:58|DEBUG: stderr:Invalid maximum heap size: -Xmx-196m Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Friday, January 14, 2022 10:45 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

my bad! cleaned output dir and reran with test data and adap - got output! going to try with a subset of our data next

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Friday, January 14, 2022 10:20 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Could you clean the output folder and retry just letting the parameters.txt file, it seems like you have artifact from an old processing. I think it should solve this.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1013217693&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=R76ZWJpJw0wZ3M73Opv4lN3OiQkaiJ38E1mxjuvL0mI&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC34KYPIJBF6JY7HL63UWA5LPANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=Gz-_aPcErVVUPngjtx5HOr5730yxPGJ2v0atI551_Ww&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=XYZ0TCuQXqa6TaxLskGG4oFeSplIH5yEi68JhjCnPIM&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=_7ewMiDRGqO0ICONO4zy-ytpamIYexf2UV4637WMRPg&e=. You are receiving this because you were mentioned.Message ID: @.***>

[ammorse]

should the java parameter not have a hyphen? -Xmx196m instead of -Xmx-196m?

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Friday, January 14, 2022 11:01 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

with my data I'm getting a Java error:

INFO: Using cached SIF image 2022-01-14|10:59:53|INFO: Total memory available: 376406 and 72 cores. The workflow will use 4 Mb by core on 12 cores. 2022-01-14|10:59:53|INFO: Guessing polarity from file:b1_aos_129.mzML 2022-01-14|10:59:53|DEBUG: Rscript /pylcmsprocessing/Rscript/get_polarity.R "/input/b1_aos_129.mzML" "/output/polarity" 2022-01-14|10:59:55|INFO: Polarity detected: positive 2022-01-14|10:59:55|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:55|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:56|INFO: STEP: initialisation TOTAL_TIME:2.48s LAST_STEP:2.48s 2022-01-14|10:59:56|INFO: An ADAP batch file has been generated in the /output directory, you ca use it to refine peakpicking parameters using MZmine. 2022-01-14|10:59:56|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:56|DEBUG: Rscript /pylcmsprocessing/Rscript/createSQLiteexperiment.R -d '/input' -b '/output/temp_processing_db.sqlite' 2022-01-14|10:59:57|INFO: Building input 2022-01-14|10:59:57|INFO: Computing MZmine parameters 2022-01-14|10:59:58|INFO: 0 existing peak picking 11 added. 2022-01-14|10:59:58|INFO: Building softwares 2022-01-14|10:59:58|INFO: Building peakpicking 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_1_e7ce7e8c6b7cb3d7d48fec2c7d71ebec.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_2_970dc76067207d1b924d080e643d84aa.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_3_4a617aa20e4f048f0cdc85d5559d7783.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_4_c96b35725531166fbfd80129e0080993.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_5_2eb6635caec00b3cd7344bc8f5cdac4f.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_6_d8eaa1acf475e1ceaa29dce505a2e374.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_7_08577539ac4063c4667e9f24375d02df.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_8_95f4493cd78798cb00428dd4c0301f9c.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_9_92d8c6e96856e8b1044ded7b67752030.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_10_2cb78523b3e947fcd9ae0c93e8bd7979.xml" 2022-01-14|10:59:58|DEBUG: /MZmine-2.52-Linux/startMZmine-Linux "/output/ADAP/xml/xml_11_91ad051e8c2a9f4eb5fd74602a4b485c.xml" 2022-01-14|10:59:58|DEBUG: stderr:Invalid maximum heap size: -Xmx-196m Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Morse,Alison Meryl @.> Sent: Friday, January 14, 2022 10:45 AM To: zamboni-lab/SLAW @.>; zamboni-lab/SLAW @.> Cc: Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

my bad! cleaned output dir and reran with test data and adap - got output! going to try with a subset of our data next

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Friday, January 14, 2022 10:20 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

Could you clean the output folder and retry just letting the parameters.txt file, it seems like you have artifact from an old processing. I think it should solve this.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1013217693&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=R76ZWJpJw0wZ3M73Opv4lN3OiQkaiJ38E1mxjuvL0mI&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWC34KYPIJBF6JY7HL63UWA5LPANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=Gz-_aPcErVVUPngjtx5HOr5730yxPGJ2v0atI551_Ww&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=XYZ0TCuQXqa6TaxLskGG4oFeSplIH5yEi68JhjCnPIM&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=03bBx7ZALbawNoGBZUgW8FunxAH38_3rweRVgUNyQR1F29Sh_15YvFcfntI1pVWz&s=_7ewMiDRGqO0ICONO4zy-ytpamIYexf2UV4637WMRPg&e=. You are receiving this because you were mentioned.Message ID: @.***>

[adelabriere]

You are right on the hyphen. You seem to have passed too little memory The workflow will use 4 Mb by core on 12 cores, did you use the -e MEMORY=XXX ? If so increase it.

[ammorse]

Ah, I see. I increased the memory and it now starts java but there are still some java errors . Runs for a minute or so then fails - see attached log file.

A

---

Alison Morse, PhD 2033 Mowry Rd, Room 120A Molecular Genetics and Microbiology University of Florida 32611 Gainesville, FL 32611 352-273-8123

---

From: Alexis Delabriere @.> Sent: Friday, January 14, 2022 11:10 AM To: zamboni-lab/SLAW @.> Cc: Morse,Alison Meryl @.>; Mention @.> Subject: Re: [zamboni-lab/SLAW] singularity issue when run adap (Issue #11)

[External Email]

You are right on the hyphen. You seem to have passed too little memory The workflow will use 4 Mb by core on 12 cores, did you use the -e MEMORY=XXX ? If so increase it.

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_zamboni-2Dlab_SLAW_issues_11-23issuecomment-2D1013257686&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=2CrQNuw8eZOFJyFCdVnUL-aWpm_jtO4g-_Gxngob0yhjV3kelVIHhIjrhwYdhEec&s=XRB-9nQbZ8VlRGLpdrNL3wjbvfBgA4dDQvsm84bYCCA&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABZYWCYFDLZHX2KVOTBPN2LUWBDF7ANCNFSM5LURFDOQ&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=2CrQNuw8eZOFJyFCdVnUL-aWpm_jtO4g-_Gxngob0yhjV3kelVIHhIjrhwYdhEec&s=bNUqnPGOKaYeHPLXt1AfIpJW1Q6mthUf8acgye14_VY&e=. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.proofpoint.com/v2/url?u=https-3A__apps.apple.com_app_apple-2Dstore_id1477376905-3Fct-3Dnotification-2Demail-26mt-3D8-26pt-3D524675&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=2CrQNuw8eZOFJyFCdVnUL-aWpm_jtO4g-_Gxngob0yhjV3kelVIHhIjrhwYdhEec&s=tPsAW64kayPwLb58PqA6oCjNxd6w19EVowshoPQOXmc&e= or Androidhttps://urldefense.proofpoint.com/v2/url?u=https-3A__play.google.com_store_apps_details-3Fid-3Dcom.github.android-26referrer-3Dutm-5Fcampaign-253Dnotification-2Demail-2526utm-5Fmedium-253Demail-2526utm-5Fsource-253Dgithub&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vQAjqof3dNfcykMkcJWPXg&m=2CrQNuw8eZOFJyFCdVnUL-aWpm_jtO4g-_Gxngob0yhjV3kelVIHhIjrhwYdhEec&s=sqfbxIn-llHcJbA8nqL-e3ZJYGzcigb2epOnF7BewfQ&e=. You are receiving this because you were mentioned.Message ID: @.***>

[adelabriere]

Thanks for the test @ammorse , I still don t see the attached log. I don t see anything attached. Could you also do a test with openMS ? It is the fastest just to be sure that your issues are related to ADAP and not something else.

[ammorse]

uploading log via github rather than email : testBrieData_adap.log

[adelabriere]

Thanks I see it now ! I never have never experienced this issue, it seems to be related to a specific permission problem on your machine similar to this one: https://stackoverflow.com/questions/67732682/how-to-change-dconf-directory So maybe adding -B /run/user/your_username will help. Is there anything specific in your machine singularity setup ?

[ammorse]

I tried your suggestion - see attached updated log file. It's odd the test data runs on my machine but not a set of my data. I'm using singularity 3.8.3.
testBrieData_adap.log

[adelabriere]

@ammorse thanks we are getting there, the mzmine error just indicates that there is no peak detected at all, all the problematic errors are gone. It is an mzmine thing not a SLAW thing. This just means that the default parameters for ADAP are not adapted for you, I will add a message for this, I admit that ADAP is the one I use the least so it is clearly less polished. SLAW should be able to find better parameters if you just set need_optimization to true.

I guess that the previous problem could be related to the location form which you launch singularity.

[ammorse]

Thanks Alexis! Will try with optimization

[ammorse]

Got it to run successfully with a subset of our data!!! Thanks Alexis! Alison