'SpecLibGen' Error

[melechco]

I am trying to generate a library but it failed (both Windows and Linux). Everything is updated. Thanks! log_2020-02-06_18-18-43.txt

[fcyu]

Thanks for your interest in FragPipe and MSFragger.

@guoci Can you take a look when you have time?

@melechco May I ask a not-so-relevant question: could you help to check if your data was from high resolution MS2?

Thanks,

Fengchao

[anesvi]

Guo Ci can you take a look. Things looked fine until one of the last steps

Sent from my iPhone

On Feb 6, 2020, at 9:21 AM, melechco notifications@github.com wrote:

 External Email - Use Caution

I am trying to generate a library but it failed (both Windows and Linux). Everything is updated. Thanks! log_2020-02-06_18-18-43.txthttps://github.com/Nesvilab/FragPipe/files/4165538/log_2020-02-06_18-18-43.txt

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM65RM5727L76JXK3PX3RBQMDXA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4ILQ27IA, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62VMJ5JOTJERJW7MX3RBQMDXANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[melechco]

Thanks for your quick response! Yes, the data were acquired in high resolution (MS1 and MS2, Q-E HF-X). Thanks

On Thu, Feb 6, 2020 at 11:26 AM Fengchao notifications@github.com wrote:

Thanks for your interest in FragPipe and MSFragger.

@guoci https://github.com/guoci Can you take a look when you have time?

@melechco https://github.com/melechco May I ask a not-so-relevant question: could you help to check if your data was from high resolution MS2?

Thanks,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7CVXZIOEYZLWGJ3AXTRBQMZJA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEK7MZIQ#issuecomment-582929570, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7DE6ZW55K6U3RACA2TRBQMZJANCNFSM4KQ5W5BA .

[anesvi]

Some quick observations

I think there are files where only few peptides were identified and PeptideProphet failed

This could cause a crash (Guo Ci - maybe we can find a way to skip pep.xml with no peptides identified with high probability)

But I am not sure why you have such runs. I noticed you used 5 ppm mass tolerance for precursor. It is too narrow. Try with 20ppm.

Alexey

Sent from my iPhone

On Feb 6, 2020, at 9:31 AM, melechco notifications@github.com wrote:

 External Email - Use Caution Thanks for your quick response! Yes, the data were acquired in high resolution (MS1 and MS2, Q-E HF-X). Thanks

On Thu, Feb 6, 2020 at 11:26 AM Fengchao notifications@github.com wrote:

Thanks for your interest in FragPipe and MSFragger.

@guoci https://github.com/guoci Can you take a look when you have time?

@melechco https://github.com/melechco May I ask a not-so-relevant question: could you help to check if your data was from high resolution MS2?

Thanks,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7CVXZIOEYZLWGJ3AXTRBQMZJA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEK7MZIQ#issuecomment-582929570, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7DE6ZW55K6U3RACA2TRBQMZJANCNFSM4KQ5W5BA .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM63CDZQPA5LQ2OFCGQDRBQNM7A5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEK7NM3Q#issuecomment-582932078, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62OQLFAUFR5JBEW53LRBQNM7ANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[melechco]

Thanks Dr. Nesvizhskii, The data came from a fractionation experiment (24 fractions) and some of them have few peptides. I've been using only 5 ppm to try to be more stringent. Our instrument is well calibrated and typically we've got sub 2 ppm. We would like to include only nice spectra in this library. We've been using SearchGui/Peptide Shaker and Skyline and it seemed to us to improve library quality. We will reprocess using broader tolerances.

[anesvi]

You can share a few files with us, we can take a look on our side too

We are wondering why our calibration step selects The highest (30ppm ) tolerance for ms2. Usually it is below 20

Sent from my iPhone

On Feb 6, 2020, at 9:52 AM, melechco notifications@github.com wrote:

 External Email - Use Caution

Thanks Dr. Nesvizhskii, The data came from a fractionation experiment (24 fractions) and some of them have few peptides. I've been using only 5 ppm to try to be more stringent. Our instrument is well calibrated and typically we've got sub 2 ppm. We would like to include only nice spectra in this library. We've been using SearchGui/Peptide Shaker and Skyline and it seemed to us to improve library quality. We will reprocess using broader tolerances.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM6YX3SV2HOZ7VJCLGDLRBQP2ZA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEK7PYGY#issuecomment-582941723, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63LS2YKIPUXXVFAJSTRBQP2ZANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[melechco]

Same problem searching with 20 ppm. How many mzML files would help? Can I share mzML within GitHub? Thanks log-fragpipe-run-at_2020-02-06_20-21-37.log

[fcyu]

@melechco Can you send me your email address? I can share a MBox folder with you to upload the data.

My email address is yufe@umich.edu

Thanks,

Fengchao

[anesvi]

Looks like the error is not with empty pep.xml files. I was wrong

I see this

SpecLibGen [Work dir: /home/valdemir/Data/plasmaproteomics_15min/Fragpipe_closedsearch20ppm] /usr/bin/python3.7 -u /tmp/fragpipe/speclib/gen_con_spec_lib.py /home/valdemir/Data/FASTA/2019-08-30-td-rev-UP000005640.fas /home/valdemir/Data/plasmaproteomics_15min/Fragpipe_closedsearch20ppm /home/valdemir/Data/plasmaproteomics_15min/Fragpipe_closedsearch20ppm/combined.prot.xml /home/valdemir/Data/plasmaproteomics_15min/Fragpipe_closedsearch20ppm True /usr/local/bin/philosopher Traceback (most recent call last): File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 702, in main0() File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 535, in main0 subprocess.run(spectrast_cmd(pep_ion_minprob), cwd=os_fspath(output_directory), check=True) File "/usr/lib/python3.7/subprocess.py", line 472, in run with Popen(*popenargs, **kwargs) as process: File "/usr/lib/python3.7/subprocess.py", line 775, in init restore_signals, start_new_session) File "/usr/lib/python3.7/subprocess.py", line 1522, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: '/tmp/fragpipe/speclib/linux/spectrast'

I think something with permissions. Guo Ci needs to take a look, or Dmitry

Alexey

From: Fengchao notifications@github.com Sent: Thursday, February 6, 2020 1:01 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/FragPipe] 'SpecLibGen' Error (#166)

External Email - Use Caution

@melechcohttps://github.com/melechco Can you send me your email address? I can share a MBox folder with you to upload the data.

My email address is yufe@umich.edumailto:yufe@umich.edu

Thanks,

Fengchao

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM6YTRZHXJN22M7PPVE3RBRF5PA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELAF6EY#issuecomment-583032595, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6YYE7J6ZLM6V6IFGX3RBRF5PANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[guoci]

@melechco try this fix https://drive.google.com/file/d/15EwKVm4tajyIjG6jvuaaQti6fhebuwa_/view?usp=sharing

[melechco]

Just an update... I'm going to upload the data from home this weekend because the firewall is blocking everything. Thanks!

On Thu, Feb 6, 2020 at 9:26 AM Fengchao notifications@github.com wrote:

Thanks for your interest in FragPipe and MSFragger.

@guoci https://github.com/guoci Can you take a look when you have time?

@melechco https://github.com/melechco May I ask a not-so-relevant question: could you help to check if your data was from high resolution MS2?

Thanks,

Fengchao

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7CVXZIOEYZLWGJ3AXTRBQMZJA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEK7MZIQ#issuecomment-582929570, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7DE6ZW55K6U3RACA2TRBQMZJANCNFSM4KQ5W5BA .

[prvst]

@guoci you can try using Box to request him/her for a file, we can send the file upload request from our accounts.

[melechco]

Hi all, I've just finished processing with the updated FragPiep-12.2.jar. It advanced in the speclib generation process but interrupted in the middle. This evening I'll upload mzML files from home. Thank you all! Have a nice weekend!

log_2020-02-07_22-47-01.txt

[guoci]

@melechco Please send me a tar.gz of your /tmp/fragpipe/ directory, through the Box invite.

[melechco]

Hi. I upload it in two large tar.gz this weekend. They will uncompress into 48 files from two fractionation experiment and could be processed together. Thanks

[fcyu]

@guoci Did you solve the problem?

Thanks,

Fengchao

[guoci]

@melechco I am still waiting for your file.

[melechco]

Hi @guoci, I uploaded it. Is there something wrong with it?

[image: image.png]

On Wed, Feb 12, 2020 at 2:21 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco I am still waiting for your file.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7CHHQGFLLEWOLEP3ODRCQVZXA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELRTZVA#issuecomment-585317588, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7CVGZGO3TSQQBJFUU3RCQVZXANCNFSM4KQ5W5BA .

[guoci]

@melechco Please send me a tar.gz of your /tmp/fragpipe/ directory, through the Box invite.

I need the above.

[melechco]

Done. Thanks!

On Wed, Feb 12, 2020 at 3:20 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco Please send me a tar.gz of your /tmp/fragpipe/ directory, through the Box invite. I need the above.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7H3ILMN66WRKF6SMTTRCQ4XPA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELR3BLQ#issuecomment-585347246, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7HCJKBRFLTQ6NWIJFTRCQ4XPANCNFSM4KQ5W5BA .

[guoci]

@melechco Thanks for the uploads. I have updated the jar, please download it again and rerun. https://drive.google.com/file/d/15EwKVm4tajyIjG6jvuaaQti6fhebuwa_/view?usp=sharing

[AaronMillOro]

Hi everyone. I was testing FragPipe to generate Spectral libraries from DDA samples generated in a TIMS-TOF Pro. This in a Debian-based local computer. When I run DDA analysis everything goes well. But there is an error appearing each time that I try to generate a Spectral Library. I would appreciate any suggestion. Thanks!

The two logs

This try was run using the updated jar file provided by @guoci log-fragpipe-run-at_2020-02-14_11-14-42.log

This try was run using the jar FragPipe from 7 days ago log-fragpipe-run-at_2020-02-14_13-13-22.log

[fcyu]

Hi @AaronMillOro

Thanks for your interest in FragPipe and MSFragger. Current version cannot build a spectral library using timsTOF data. We will release a new version by adding another spectral library building module in the future.

Best,

Fengchao

[AaronMillOro]

Thank you for your feedback @fcyu ! Looking forward for the future module releases. I found really nice the way FragPipe exploits the pasef technology. Best regards! Aaron :shipit:

[melechco]

Hi all, I've just finished processing with the updated FragPiep-12.2.jar. It advanced in the speclib generation process but interrupted in the middle. This evening I'll upload mzML files from home. Thank you all! Have a nice weekend!

log_2020-02-07_22-47-01.txt

[melechco]

Hi, I've just finished with the updated jar but it is still returning an error. I'll upload this /tmp/fragpipe this evening. Thanks a lot!

On Thu, Feb 13, 2020 at 3:19 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco Thanks for the uploads. I have updated the jar, please download it again and rerun.

https://drive.google.com/file/d/15EwKVm4tajyIjG6jvuaaQti6fhebuwa_/view?usp=sharing

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7BAFEYMMRLANRF52HDRCWTL3A5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELWO3EI#issuecomment-585952657, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7FHUIYUGXNEFMZYWN3RCWTL3ANCNFSM4KQ5W5BA .

[guoci]

I can see the error in your log: PermissionError: [Errno 13] Permission denied: '/tmp/fragpipe/speclib/linux/spectrast' which I have fixed in the updated jar. In fact, I can run /tmp/fragpipe/speclib/linux/spectrast successfully. Can you delete /tmp/fragpipe/speclib/, then restart FragPipe?

[melechco]

Hi Guoci, I deleted /tmp/fragpipe/speclib/, restarted FragPipe and run again. Unfortunatelly it is stopping at SpecLibGen. I´m going to upload this evening. Thanks once again.

On Tue, Feb 18, 2020 at 1:53 PM guoci notifications@github.com wrote:

I can see the error in your log: PermissionError: [Errno 13] Permission denied: '/tmp/fragpipe/speclib/linux/spectrast' which I have fixed in the updated jar. In fact, I can run /tmp/fragpipe/speclib/linux/spectrast successfully. Can you delete /tmp/fragpipe/speclib/, then restart FragPipe?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7CXJHBOGKULTGT5S6LRDQHANA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMCXW7A#issuecomment-587561852, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7EZL6QD7XKDB33STALRDQHANANCNFSM4KQ5W5BA .

[guoci]

@melechco thanks for the upload. Can you try the following? It will take a minute.

1. Start Fragpipe.
2. open a python terminal, paste the following, and show me the output. import subprocess;subprocess.run('/tmp/fragpipe/speclib/linux/spectrast')
3. also in a shell type stat /tmp/fragpipe/speclib/linux/spectrast and show the output

[melechco]

Sure! Just a question: Should I just load Fragpipe and execute the python command or should I press run and execute it anytime, or only while Fragpipe is doing the spectral lib generation? Thanks!

On Wed, Feb 19, 2020 at 2:38 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks for the upload. Can you try the following? It will take a minute.

1. Start Fragpipe.
2. open a python terminal, paste the following, and show me the output. import subprocess;subprocess.run('/tmp/fragpipe/speclib/linux/spectrast')

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7BCQ342QWSJUYMPW3TRDVVCZA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMIXTYQ#issuecomment-588347874, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7HUU4YH3A4YZO25F4LRDVVCZANCNFSM4KQ5W5BA .

[guoci]

@melechco Just start FragPipe, make sure the spectral library generation is enabled, no need to press run.

[melechco]

The output was:

import subprocess;subprocess.run('/tmp/fragpipe/speclib/linux/spectrast') SpectraST (version 5.0, TPP v5.0.0 Typhoon, Build 201610181424-exported (Linux-x86_64)) by Henry Lam.

(I) CREATE MODE Usage: spectrast [ options ] [ ... ] where: FileNameX = Name of file containing spectra from which library is to be created. Extension specifies format of file. Supports .msp, .hlf, .pepXML (or .pep.xml or .xml), .ms2, and .splib.

Options: GENERAL OPTIONS -cF Read create options from file . If is not given, "spectrast_create.params" is assumed. NOTE: All options set in the file will be overridden by command-line options, if specified. -cN Specify output file name for .splib, .spidx and .pepidx files. -cm Remark. Add a Remark= comment to all library entries created. -cM Write all library spectra as MRM transition tables. Leave blank for default. (Turn off with -cM!) -cT Use probability table in . Only those peptide ions included in the table will be imported. A probability table is a text file with one peptide ion in the format AC[160]DEFGHIK/2 per line. If a probability is supplied following the peptide ion separated by a tab, it will be used to replace the original probability of that library entry. -cO Use protein list in . Only those peptide ions associated with proteins in the list will be imported. A protein list is a text file with one protein identifier per line. If a number X is supplied following the protein separated by a tab, then at most X peptide ions associated with that protein will be imported.

     PEPXML IMPORT OPTIONS (Applicable with .pepXML files)
     -cP<prob>    Include all spectra identified with probability no

less than in the library. -cq (Only PepXML import) Only include spectra with global FDR no greater than in the library. -cn Specify a dataset identifier for the file to be imported. -co Add the originating mzXML file name to the dataset identifier. Good for keeping track of in which MS run the peptide is observed. (Turn off with -co!) -cg Set all asparagines (N) in the motif NX(S/T) as deamidated (N[115]). Use for glycocaptured peptides. (Turn off with -cg!). -cI Set the instrument and acquisition settings of the spectra (in case not specified in data files). Examples: -cICID, -cIETD, -cICID-QTOF, -cIHCD. The latter two are treated as high-mass accuracy spectra.

     LIBRARY MANIPULATION OPTIONS (Applicable with .splib files)
     -cf<pred>    Filter library. Keep only those entries satisfying

the predicate .

should be a C-style predicate in quotes. -cJU Union. Include all the peptide ions in all the files. -cJI Intersection. Only include peptide ions that are present in all the files. -cJS Subtraction. Only include peptide ions in the first file that are not present in any of the other files. -cJH Subtraction of homologs. Only include peptide ions in the first file that do not have any homologs with same charge and similar m/z in any of the other files. -cJA Appending. Each peptide ion is added from only one library: the first file in the argument list that contains that peptide ion. Useful for keeping existing consensus spectra unchanged while adding only previously unseen peptide ions. -cAB Best replicate. Pick the best replicate of each peptide ion. -cAC Consensus. Create the consensus spectrum of all replicate spectra of each peptide ion. -cAQ Quality filter. Apply quality filters to library. IMPORTANT: Quality filter can only be applied on a SINGLE .splib file with no peptide ion represented by more than one spectrum. -cAD Create artificial decoy spectra. -cAN Sort library entries by descending number of replicates used (tie-breaking by probability). -cAM Create semi-empirical spectra based on allowable modifications specified by -cx option. -cQ Produce reduced spectra of at most peaks. Inactive with -cAQ and -cAD. -cD Refresh protein mappings of each library entry against the protein database (Must be in .fasta format). -cu Delete entries whose peptide sequences do not map to any protein during refreshing with -cD option. When off, unmapped entries will be marked with Protein=0/UNMAPPED but retained in library. (Turn off with -cu!). -cd Delete entries whose peptide sequences map to multiple proteins during refreshing with -cD option. (Turn off with -cd!). CONSENSUS/BEST-REPLICATE OPTIONS (Applicable with -cAC and -cAB options) -cr Minimum number of replicates required for each library entry. Peptide ions failing to have originated from enough replicates will be excluded from library when creating consensus/best-replicate library. QUALITY FILTER OPTIONS (Applicable with -cAQ option) -cr Replicate quorum. Its value affects behavior of quality filter (see below). -cL Specify the stringency of the quality filter. -cl -cL specifies the level for removal, -cl specifies the level for marking. = 0: No filter. = 1: Remove/mark impure spectra. = 2: Also remove/mark spectra with a spectrally similar counterpart in the library that is better. = 3: Also remove/mark inquorate entries (defined with -cr) that share no peptide sub-sequences with any other entries in the library. = 4: Also remove/mark all singleton entries. = 5: Also remove/mark all inquorate entries (defined with -cr). DECOY CREATION OPTIONS (Applicable with -cAD option) -cc Concatenate real and decoy libraries. (Turn off with -cc!) -cy Specify the (decoy / real) size ratio. Must be an integer. SEMI-EMPIRICAL SPECTRUM CREATION OPTIONS (Applicable with -cAM option) -cx Specify allowable modification tokens used to generate new peptide ions for which semi-empirical spectra are to be created. (e.g. -cx"K[136]" for static mod of +6 heavy lysines, -cx"MM[147]" for variable mod of methionine oxidation.) OTHER ADVANCED OPTIONS Type "spectrast -c_" for a full list of advanced (and obscure and not-so-useful) options. (II) SEARCH MODE Usage: spectrast [ options ] [ ... ] where: SearchFileNameX = Name(s) of file containing unknown spectra to be searched. (Extension specifies format of file. Supports .mzXML, .mzData, .dta and .msp) Options: GENERAL OPTIONS -sF Read search options from file. If is not given, "spectrast.params" is assumed. NOTE: All options set in the file will be overridden by command-line options, if specified. -sL Specify library file. must have .splib extension. The existence of the corresponding .spidx file of the same name in the same directory is assumed. -sD Specify a sequence database file. must be in .fasta format. This will not affect the search in any way, but this information will be included in the output for any downstream data processing. -sT Specify the type of the sequence database file. must be either "AA" or "DNA". -sR Cache all entries in RAM. (Turn off with -sR!) Requires a lot of memory (the library will usually be loaded almost in its entirety), but speeds up search for unsorted queries. -sP Multi-threaded search (one thread per file). Specify the number of threads to use. (Turn off with -sP!) If multi-threading is enabled, -sR (Cache all entries in RAM) is automatically turned on. -sS Only search a subset of the query spectra in the search file. Only query spectra with names matching a line of will be searched. CANDIDATE SELECTION AND SCORING OPTIONS -sM Specify precursor m/z tolerance. is the m/z tolerance within which candidate entries are compared to the query. -sA Use isotopically averaged mass instead of monoisotopic mass. (Turn of with -sA!) -sz Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum. OUTPUT AND DISPLAY OPTIONS -sE Output format. The search result will be written to a file with the same base name as the search file, with extension = txt : Fixed-width text format. = xls : Tab-delimited text format. = pep.xml or xml or pepXML : PepXML format. = html : HTML format. -sO Write output file to instead of the same directory as the query data file. OTHER ADVANCED OPTIONS Type "spectrast -s_" for a full list of advanced (and obscure and not-so-useful) options. Miscellaneous Options: -V Verbose mode. -Q Quiet mode. -L Specify name of log file. Default is "spectrast.log". -M Specify name of user-defined modifications file. Default is "spectrast.usermods". CompletedProcess(args='/tmp/fragpipe/speclib/linux/spectrast', returncode=1) On Wed, Feb 19, 2020 at 12:53 PM guoci wrote: > @melechco Just start FragPipe, make sure > the spectral library generation is enabled, no need to press run. > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > , > or unsubscribe > > . >

[guoci]

@melechco In your log from your latest run, did you see the following line? PermissionError: [Errno 13] Permission denied: '/tmp/fragpipe/speclib/linux/spectrast'

[melechco]

No.

SpectraST started at Wed Feb 19 00:43:10 2020. Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_1.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_10.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_11.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_12.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_13.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_14.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_15.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_16.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_17.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_18.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_19.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_2.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_20.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_21.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_22.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_23.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_24.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_3.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_4.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_5.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_6.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_7.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_8.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-B_pHgrad15min_9.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_1.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_10.pep.xml"...500...1000...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_11.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_12.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_13.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_14.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_15.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_16.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_17.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_18.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_19.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_2.pep.xml"...500...1000...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_20.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_21.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_22.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_23.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_24.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_3.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_4.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_5.pep.xml"...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_6.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_7.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_8.pep.xml"...500...DONE! Processing "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/interact-D_pHgrad15min_9.pep.xml"...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_1.mzXML'. DONE! Importing all spectra with P>=0.9514 ...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_10.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_11.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_12.mzXML'. 10%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_13.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_14.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_15.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_16.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_17.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_18.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_19.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_2.mzXML'. 20%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_20.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_21.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_22.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_23.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_24.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_3.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_4.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_5.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_6.mzXML'. 30%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_7.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_8.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_9.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_1.mzXML'. 40%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_10.mzXML'. 50%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_11.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_12.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_13.mzXML'. 60%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_14.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_15.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_16.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_17.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_18.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_19.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_2.mzXML'. 70%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_20.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_21.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_22.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_23.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_24.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_3.mzXML'. 80%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_4.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_5.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_6.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_7.mzXML'. 90%...Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_8.mzXML'. Failed to open input file '/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/D_pHgrad15min_9.mzXML'. DONE!

Library file "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/input000.splib" created. M/Z Index file "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/input000.spidx" created. Peptide Index file "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/input000.pepidx" created.

Total number of spectra in library: 16542 Total number of distinct peptide ions in library: 4473 Total number of distinct stripped peptides in library: 3119

CHARGE +1: 0 ; +2: 11082 ; +3: 4295 ; +4: 1011 ; +5: 143 ; >+5: 11 ; Unk: 0 TERMINI Tryptic: 16499 ; Semi-tryptic: 43 ; Non-tryptic: 0 PROBABILITY >0.9999: 7825 ; 0.999-0.9999: 1448 ; 0.99-0.999: 4098 ; 0.9-0.99: 3171 ; <0.9: 0 NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 16542 MODIFICATIONS C,Carbamidomethyl: 5959 M,Oxidation: 2275 n,Acetyl: 8

Total Run Time = 61 seconds. SpectraST finished at Wed Feb 19 00:44:11 2020 without error. Executing:

Generate .pepidx file

/usr/bin/python3.7 /tmp/fragpipe/speclib/spectrast_gen_pepidx.py -i input.splib -o input_irt.splib

outfiles: input_irt.splib, input_irt.csv

Consolidate the library into a single consensus spectrum entry for each

peptide sequence. /tmp/fragpipe/speclib/linux/spectrast -M spectrast.usermods -cAC -c_BIN! -cIHCD -cNoutput_file_irt_con000 input_irt.splib

outfile:output_file_irt_con000.splib

Unite runs

/usr/bin/python3.7 /tmp/fragpipe/speclib/unite_runs.py output_file_irt_con000.splib output_file_irt_con001.splib

outfile:output_file_irt_con001.splib

Traceback (most recent call last): File "/tmp/fragpipe/speclib/spectrast_gen_pepidx.py", line 38, in import matplotlib as mpl ModuleNotFoundError: No module named 'matplotlib' SpectraST started at Wed Feb 19 00:44:13 2020. Creating CONSENSUS library from "/home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/input_irt.splib"

Library file "output_file_irt_con000.splib" created. M/Z Index file "output_file_irt_con000.spidx" created. Peptide Index file "output_file_irt_con000.pepidx" created.

Total number of spectra in library: 0 Total number of distinct peptide ions in library: 0 Total number of distinct stripped peptides in library: 0

CHARGE +1: 0 ; +2: 0 ; +3: 0 ; +4: 0 ; +5: 0 ; >+5: 0 ; Unk: 0 TERMINI Tryptic: 0 ; Semi-tryptic: 0 ; Non-tryptic: 0 PROBABILITY >0.9999: 0 ; 0.999-0.9999: 0 ; 0.99-0.999: 0 ; 0.9-0.99: 0 ; <0.9: 0 NREPS 20+: 0 ; 10-19: 0 ; 4-9: 0 ; 2-3: 0 ; 1: 0 MODIFICATIONS None

Total Run Time = 1 seconds. SpectraST finished at Wed Feb 19 00:44:14 2020 with 1 error(s): CREATE: Cannot open SPLIB file "input_irt.splib" for reading. File skipped.

Unite runs done Executing:

iRT alignment

/usr/bin/python3.7 /usr/local/bin/spectrast2spectrast_irt.py --kit LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424,VEATFGVDESNAK:13.1078,YILAGVENSK:22.3798,TPVISGGPYEYR:28.9999,TPVITGAPYEYR:33.6311,DGLDAASYYAPVR:43.2819,ADVTPADFSEWSK:54.969,GTFIIDPGGVIR:71.3819,GTFIIDPAAVIR:86.7152,LFLQFGAQGSPFLK:98.0897 --rsq_threshold=0.25 -r -i output_file_irt_con001.splib -o output_file_irt_con.splib

outfile:output_file_irt_con.splib

Skipping iRT alignment

Executing:

Filter the consensus splib library into a transition list

/usr/bin/python3.7 /usr/local/bin/spectrast2tsv.py -m /home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/spectrast2tsv_additional_mods_path.tsv -g -17.03,-18.01 -l 250,2000 -s b,y -x 1,2 -o 3 -n 6 -p 0.05 -d -e -k openswath -a output_irt_con.tsv output_file_irt_con.splib

outfile:output_irt_con.tsv

Traceback (most recent call last): File "/usr/local/bin/spectrast2tsv.py", line 1263, in main(sys.argv[1:]) File "/usr/local/bin/spectrast2tsv.py", line 867, in main offset , spectrum = spectrastlib.read_sptxt_with_offset(sptxtfile,offset) File "/usr/local/lib/python3.7/dist-packages/msproteomicstoolslib/format/speclib_db_lib.py", line 459, in read_sptxt_with_offset s.parse_sptxt( stack ) File "/usr/local/lib/python3.7/dist-packages/msproteomicstoolslib/format/speclib_db_lib.py", line 940, in parse_sptxt self.sequence = re.sub( '[^A-Z]', '', self.name ) AttributeError: 'Spectra' object has no attribute 'name' Traceback (most recent call last): File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 702, in main0() File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 561, in main0 subprocess.run(adjust_command(spectrast_cmds_part3), shell=True, cwd=os_fspath(output_directory), check=True) File "/usr/lib/python3.7/subprocess.py", line 487, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '

Filter the consensus splib library into a transition list

/usr/bin/python3.7 /usr/local/bin/spectrast2tsv.py -m /home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/spectrast2tsv_additional_mods_path.tsv -g -17.03,-18.01 -l 250,2000 -s b,y -x 1,2 -o 3 -n 6 -p 0.05 -d -e -k openswath -a output_irt_con.tsv output_file_irt_con.splib

outfile:output_irt_con.tsv

' returned non-zero exit status 1. Masslimits: [250.0, 2000.0] Modifications used : ['C[160]', 'M[147]', 'W[202]', 'H[153]', 'K[136]', 'R[166]', 'E[111]', 'Q[111]', 'C[143]', 'n[43]', 'S[167]', 'T[181]', 'Y[243]', 'N[115]', 'Q[129]', 'C[149]', 'D[131]', 'K[144]', 'Y[179]', 'R[172]', 'N[130]', 'P[113]', 'C[119]', 'N[317]', 'N[349]', 'C[222]', 'c[17]'] No swath windows set. Reading : output_file_irt_con.splib Process 'SpecLibGen' finished, exit code: 1

Process returned non-zero exit code, stopping SpecLibGen java -cp /home/valdemir/Software/FragPipe-12.2.jar umich.msfragger.util.FileDelete /home/valdemir/Data/plasmaproteomics_15min/closedsearch20200218/B_pHgrad15min_4.mzML

Cancelling 49 remaining tasks

On Wed, Feb 19, 2020 at 3:04 PM guoci <notifications@github.com> wrote:

> @melechco <https://github.com/melechco> In your log from your latest run,
> did you see the following line?
> PermissionError: [Errno 13] Permission denied:
> '/tmp/fragpipe/speclib/linux/spectrast'
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DHAKFNJWKZGAG4L53RDVYC7A5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMI2ZXY#issuecomment-588360927>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ALRTS7H3WQOPNMBKTWZECO3RDVYC7ANCNFSM4KQ5W5BA>
> .
>

[guoci]

@melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

[anesvi]

Guo Ci and Dmitry, can you create a tutorial for installing/running FragPipe on Linux? What python modules need to be installed?

I think our current document https://msfragger.nesvilab.org/tutorial_setup_fragpipe.html covers only Windows

Thanks Alexey

From: guoci notifications@github.com Sent: Wednesday, February 19, 2020 3:35 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/FragPipe] 'SpecLibGen' Error (#166)

External Email - Use Caution

@melechcohttps://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM62VFZCL723B5GTJ7DTRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6Y2UPSFCGOMDGKITH3RDWJVTANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[melechco]

Excellent! Thanks for your dedication Guoci. Very much appreciated!

On Wed, Feb 19, 2020 at 3:34 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7GFYSU4SY4SCRT3JLLRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7CZIEFZXADWEJDKC53RDWJVTANCNFSM4KQ5W5BA .

[anesvi]

Were you finally able to run it? We appreciate your feedback, and thank you for using the tools. Best, Alexey

Sent from my iPhone

On Feb 19, 2020, at 7:10 PM, melechco notifications@github.com wrote:

 External Email - Use Caution Excellent! Thanks for your dedication Guoci. Very much appreciated!

On Wed, Feb 19, 2020 at 3:34 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7GFYSU4SY4SCRT3JLLRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7CZIEFZXADWEJDKC53RDWJVTANCNFSM4KQ5W5BA .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM65PU3X5Y4JAWPTGB7LRDXC5PA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMKGW5Q#issuecomment-588540790, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM63INPMMRS2DK3TZMQLRDXC5PANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[melechco]

Sorry for the delay. It is ultrafast! Amazing! I still exploring the output. Should I expect a .splib file or tsvs? Thank you

On Sat, Feb 22, 2020 at 5:00 PM Alexey Nesvizhskii notifications@github.com wrote:

Were you finally able to run it? We appreciate your feedback, and thank you for using the tools. Best, Alexey

Sent from my iPhone

On Feb 19, 2020, at 7:10 PM, melechco notifications@github.com wrote:

 External Email - Use Caution Excellent! Thanks for your dedication Guoci. Very much appreciated!

On Wed, Feb 19, 2020 at 3:34 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7GFYSU4SY4SCRT3JLLRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALRTS7CZIEFZXADWEJDKC53RDWJVTANCNFSM4KQ5W5BA>

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM65PU3X5Y4JAWPTGB7LRDXC5PA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMKGW5Q#issuecomment-588540790>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AIIMM63INPMMRS2DK3TZMQLRDXC5PANCNFSM4KQ5W5BA>.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DNRWLTVHZQO65NJXTREGN7DA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMVLRYQ#issuecomment-590002402, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7BIJPBRBDIAOEH7MQTREGN7DANCNFSM4KQ5W5BA .

[guoci]

@melechco you should get a file named con_lib.tsv.

[anesvi]

What software are you planning to use with the spectral libraries?

Sent from my iPhone

On Feb 24, 2020, at 10:22 AM, melechco notifications@github.com wrote:

 External Email - Use Caution Sorry for the delay. It is ultrafast! Amazing! I still exploring the output. Should I expect a .splib file or tsvs? Thank you

On Sat, Feb 22, 2020 at 5:00 PM Alexey Nesvizhskii notifications@github.com wrote:

Were you finally able to run it? We appreciate your feedback, and thank you for using the tools. Best, Alexey

Sent from my iPhone

On Feb 19, 2020, at 7:10 PM, melechco notifications@github.com wrote:

 External Email - Use Caution Excellent! Thanks for your dedication Guoci. Very much appreciated!

On Wed, Feb 19, 2020 at 3:34 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7GFYSU4SY4SCRT3JLLRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALRTS7CZIEFZXADWEJDKC53RDWJVTANCNFSM4KQ5W5BA>

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM65PU3X5Y4JAWPTGB7LRDXC5PA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMKGW5Q#issuecomment-588540790>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AIIMM63INPMMRS2DK3TZMQLRDXC5PANCNFSM4KQ5W5BA>.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DNRWLTVHZQO65NJXTREGN7DA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMVLRYQ#issuecomment-590002402, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7BIJPBRBDIAOEH7MQTREGN7DANCNFSM4KQ5W5BA .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM64QJYDDKH2IOXMCDUDREPQ4LA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMYG4WY#issuecomment-590376539, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62NUKABLA5OF6QXSATREPQ4LANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[AaronMillOro]

Hi again, I wanted to test the Spectral Library generation but this time I used different files. These 8 mzML files were obtained in an Orbitrap Fusion Lumos Tribrid on DDA mode. Then I followed the recommended tutorial but it stopped in the last step

SpecLibGen [Work dir: /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary]
python3 -u /tmp/fragpipe/speclib/gen_con_spec_lib.py /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/good_database/2020-02-18-decoys-one_fasta_file.fasta /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary/combined.prot.xml /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary True /home/amillan/Documents/2020/2020_02_07_MSFragger/philosopher
Traceback (most recent call last):
  File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 101, in <module>
    spectrast2spectrast_irt_py_path = pathlib.Path(shutil.which('spectrast2spectrast_irt.py'))
  File "/usr/lib/python3.7/pathlib.py", line 1003, in __new__
    self = cls._from_parts(args, init=False)
  File "/usr/lib/python3.7/pathlib.py", line 658, in _from_parts
    drv, root, parts = self._parse_args(args)
  File "/usr/lib/python3.7/pathlib.py", line 642, in _parse_args
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
Process 'SpecLibGen' finished, exit code: 1

I ran this in a Debian workstation and installed the recommended python 3 modules.

I attach the log file here:

log-fragpipe-run-at_2020-02-25_15-49-18.log

I'd appreciate any suggestion

Thanks in advance

[anesvi]

First, and this is why it probably crashed, you need to run the Filter command. It is missing in your log. Did you unckeck ‘Generate Report’ box FragPipe Report tab? Please put it back

Second, something wrong with your fasta. Try using the database downloaded by philosopher first. 2020-02-18-decoys-one_fasta_file.fasta I see some weird warnings from ProteinProphet like: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: - WARNING: Trying to compute mass of non-residue: - WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: e WARNING: Trying to compute mass of non-residue: e WARNING: Trying to compute mass of non-residue: d WARNING: Trying to compute mass of non-residue: d WARNING: Trying to compute mass of non-residue: i WARNING: Trying to compute mass of non-residue: i WARNING: Trying to compute mass of non-residue: t

Alexey

From: Aaron Millan notifications@github.com Sent: Tuesday, February 25, 2020 10:01 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/FragPipe] 'SpecLibGen' Error (#166)

External Email - Use Caution

Hi again, I wanted to test the Spectral Library generation but this time I used different files. These 8 mzML files were obtained in an Orbitrap Fusion Lumos Tribrid on DDA mode. Then I followed the recommended tutorial but it stopped in the last step

SpecLibGen [Work dir: /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary]

python3 -u /tmp/fragpipe/speclib/gen_con_spec_lib.py /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/good_database/2020-02-18-decoys-one_fasta_file.fasta /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary/combined.prot.xml /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/MSFraggerLibrary True /home/amillan/Documents/2020/2020_02_07_MSFragger/philosopher

Traceback (most recent call last):

File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 101, in

spectrast2spectrast_irt_py_path = pathlib.Path(shutil.which('spectrast2spectrast_irt.py'))

File "/usr/lib/python3.7/pathlib.py", line 1003, in new

self = cls._from_parts(args, init=False)

File "/usr/lib/python3.7/pathlib.py", line 658, in _from_parts

drv, root, parts = self._parse_args(args)

File "/usr/lib/python3.7/pathlib.py", line 642, in _parse_args

a = os.fspath(a)

TypeError: expected str, bytes or os.PathLike object, not NoneType

Process 'SpecLibGen' finished, exit code: 1

I ran this in a Debian workstation and installed the recommended python 3 modules.

I attach the log file here:

log-fragpipe-run-at_2020-02-25_15-49-18.loghttps://github.com/Nesvilab/FragPipe/files/4250621/log-fragpipe-run-at_2020-02-25_15-49-18.log

I'd appreciate any suggestion

Thanks in advance

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM6545SUZVSNJR74MXKDREUXD3A5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM4JFIA#issuecomment-590910112, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM67ZN2TB2JM3CLX27QTREUXD3ANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[AaronMillOro]

Hi, thanks for the quick response.

I tried this time with the two recommendations:
i) selected the generate report option, and ii) downloaded the database from uniprot using philosopher (no custom database as in the previous post)

It seems to stop in the last step. Here the log file:

log-fragpipe-run-at_2020-02-26_13-41-14.log

[melechco]

Good morning, Skyline. Thanks

On Mon, Feb 24, 2020 at 8:05 PM Alexey Nesvizhskii notifications@github.com wrote:

What software are you planning to use with the spectral libraries?

Sent from my iPhone

On Feb 24, 2020, at 10:22 AM, melechco notifications@github.com wrote:

 External Email - Use Caution Sorry for the delay. It is ultrafast! Amazing! I still exploring the output. Should I expect a .splib file or tsvs? Thank you

On Sat, Feb 22, 2020 at 5:00 PM Alexey Nesvizhskii < notifications@github.com> wrote:

Were you finally able to run it? We appreciate your feedback, and thank you for using the tools. Best, Alexey

Sent from my iPhone

On Feb 19, 2020, at 7:10 PM, melechco notifications@github.com wrote:

 External Email - Use Caution Excellent! Thanks for your dedication Guoci. Very much appreciated!

On Wed, Feb 19, 2020 at 3:34 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7GFYSU4SY4SCRT3JLLRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ALRTS7CZIEFZXADWEJDKC53RDWJVTANCNFSM4KQ5W5BA>

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub<

https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM65PU3X5Y4JAWPTGB7LRDXC5PA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMKGW5Q#issuecomment-588540790>,

or unsubscribe<

https://github.com/notifications/unsubscribe-auth/AIIMM63INPMMRS2DK3TZMQLRDXC5PANCNFSM4KQ5W5BA>.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DNRWLTVHZQO65NJXTREGN7DA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMVLRYQ#issuecomment-590002402>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALRTS7BIJPBRBDIAOEH7MQTREGN7DANCNFSM4KQ5W5BA>

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM64QJYDDKH2IOXMCDUDREPQ4LA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMYG4WY#issuecomment-590376539>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AIIMM62NUKABLA5OF6QXSATREPQ4LANCNFSM4KQ5W5BA>.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DSIKHK4X5KK75LXL3RERHCVA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMZ37MY#issuecomment-590593971, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7BVI53WNF34673YCR3RERHCVANCNFSM4KQ5W5BA .

[anesvi]

if you succeed at getting con_lib.tsv in Skyline, please let us know what you did. With Skyline we have been importing interact.pep.xml files Alexey

Sent from my iPhone

On Feb 26, 2020, at 8:35 AM, melechco notifications@github.com wrote:

 External Email - Use Caution Good morning, Skyline. Thanks

On Mon, Feb 24, 2020 at 8:05 PM Alexey Nesvizhskii notifications@github.com wrote:

What software are you planning to use with the spectral libraries?

Sent from my iPhone

On Feb 24, 2020, at 10:22 AM, melechco notifications@github.com wrote:

 External Email - Use Caution Sorry for the delay. It is ultrafast! Amazing! I still exploring the output. Should I expect a .splib file or tsvs? Thank you

On Sat, Feb 22, 2020 at 5:00 PM Alexey Nesvizhskii < notifications@github.com> wrote:

Were you finally able to run it? We appreciate your feedback, and thank you for using the tools. Best, Alexey

Sent from my iPhone

On Feb 19, 2020, at 7:10 PM, melechco notifications@github.com wrote:

 External Email - Use Caution Excellent! Thanks for your dedication Guoci. Very much appreciated!

On Wed, Feb 19, 2020 at 3:34 PM guoci notifications@github.com wrote:

@melechco https://github.com/melechco thanks. The bug was resolved. The current error was caused by a missing module. Can you install the python module matplotlib and rerun?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7GFYSU4SY4SCRT3JLLRDWJVTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMJNFQQ#issuecomment-588436162>,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ALRTS7CZIEFZXADWEJDKC53RDWJVTANCNFSM4KQ5W5BA>

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub<

https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM65PU3X5Y4JAWPTGB7LRDXC5PA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMKGW5Q#issuecomment-588540790>,

or unsubscribe<

https://github.com/notifications/unsubscribe-auth/AIIMM63INPMMRS2DK3TZMQLRDXC5PANCNFSM4KQ5W5BA>.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub < https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DNRWLTVHZQO65NJXTREGN7DA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMVLRYQ#issuecomment-590002402>,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALRTS7BIJPBRBDIAOEH7MQTREGN7DANCNFSM4KQ5W5BA>

.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub< https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM64QJYDDKH2IOXMCDUDREPQ4LA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMYG4WY#issuecomment-590376539>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AIIMM62NUKABLA5OF6QXSATREPQ4LANCNFSM4KQ5W5BA>.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=ALRTS7DSIKHK4X5KK75LXL3RERHCVA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMZ37MY#issuecomment-590593971, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALRTS7BVI53WNF34673YCR3RERHCVANCNFSM4KQ5W5BA .

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/166?email_source=notifications&email_token=AIIMM6ZSL4WELUN75GKOWMTREZVZTA5CNFSM4KQ5W5BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENAHYEQ#issuecomment-591428626, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM62AK4YCWDFX7LZQZKDREZVZTANCNFSM4KQ5W5BA.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[guoci]

@AaronMillOro Please try the following jar FragPipe-12.3-build6.jar and let me know the outcome.

[AaronMillOro]

@guoci Thanx for your last message and sorry for the delay. I tested the last jar file and I got the following error message, just after the SpecLibGen line code:

Traceback (most recent call last): File "/tmp/fragpipe/speclib/gen_con_spec_lib.py", line 82, in <module> os.environ['PATH'] = pathlib.Path(sys.executable).parents[1] / 'bin' + os.pathsep + os.environ['PATH'] TypeError: unsupported operand type(s) for +: 'PosixPath' and 'str' Process 'SpecLibGen' finished, exit code: 1 Process returned non-zero exit code, stopping Workspace [Work dir: /home/amillan/Documents/2020/2020_02_17_FusionLumos_SpecLibs_MSFragger/20200228_SpectraST] /home/amillan/Documents/2020/2020_02_07_MSFragger/philosopher workspace --clean

Here the log file log-fragpipe-run-at_2020-02-28_16-03-16.log

Thanks in advance !

[guoci]

@AaronMillOro Please try the updated jar FragPipe-12.3-build7.jar.

[anesvi]

What is the latest on that? Was the issue resolved?