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GiantSpaceRobot / FindFungi

A pipeline for the identification of fungi in public metagenomics datasets
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issues with Running FindFungi-0.23.3.sh #13

Closed sqqsjc closed 4 years ago

sqqsjc commented 4 years ago

Dear Sir/Madam I am trying to use FindFungi on the example ERR675624. I have downloaded all the Kraken and blast databases, and have specified my directory paths on the FindFungi-0.23.3.sh and LowestCommonAncestor_V4.sh script files. However, when I run to : python2.7 $ScriptPath/Consensus-CrossRef-Skewness_V2.py $Dir/Processing/Consensus.sorted.$z.All-Kraken-Results.tsv $Dir/Results/BLAST_Processing/All-Skewness-Scores $Dir/Results/FinalResults$z.tsv FinalResults$z.tsv is 0 bytes in size.
How can I solve a problem and ask for your help. Thank you! Regards Qian

GiantSpaceRobot commented 4 years ago

Hi there,

Do the files $Dir/Processing/Consensus.sorted.$z.All-Kraken-Results.tsv and $Dir/Results/BLAST_Processing/All-Skewness-Scores contain data?

sqqsjc commented 4 years ago

Dear Sir/Madam, Yes, the files $Dir/Processing/Consensus.sorted.$z.All-Kraken-Results.tsv and $Dir/Results/BLAST_Processing/All-Skewness-Scores contain data. [clslzy@login3 BLAST_Processing]$ ls -hl All-Skewness-Scores 21K Jun 11 20:43 All-Skewness-Scores [clslzy@login3 Processing]$ ls -hl Consensus.sorted.ERR675624.All-Kraken-Results.tsv 12M Jun 11 20:42 Consensus.sorted.ERR675624.All-Kraken-Results.tsv but output file is empty. 0 Jun 11 20:43 Final_Results_ERR675624.tsv ouput files in ./ERR675624/FindFungi/Results: 27 Jun 11 20:43 ERR675624.gv 24 Jun 11 20:43 ERR675624.WordCloud.R 25K Jun 11 20:43 Final_Results_ERR675624_AllResults-lca.sorted.csv 142 Jun 11 20:43 Final_Results_ERR675624-lca.csv 142 Jun 11 20:43 Final_Results_ERR675624-lca.sorted.csv 0 Jun 11 20:43 Final_Results_ERR675624-taxids.txt 0 Jun 11 20:43 Final_Results_ERR675624.tsv 25K Jun 11 20:43 Final_Results_ERR675624.tsv_AllResults-lca.csv 3.0K Jun 11 20:43 Final_Results_ERR675624.tsv_AllResults-taxids.txt 13M Jun 11 20:43 Final_Results_ERR675624.tsv_AllResults.tsv

Ask for your help! Thanks! Regards Qian

GiantSpaceRobot commented 4 years ago

Hi there,

You could also try running the attached script. I'm not sure I have the correct path names for your system, but it should look something like this: python Consensus-CrossRef-Skewness_V2_test.py Processing/Consensus.sorted.ERR675624.All-Kraken-Results.tsv Results/BLAST_Processing/All-Skewness-Scores Final_Results_TEST.tsv > MyScript.log Please send me the file MyScript.log, thank you.

sqqsjc commented 4 years ago

when I run the command: python Consensus-CrossRef-Skewness_V2.py /lustre/home/acct-clslzy/clslzy/home/qqsong/myshell/findfungi/test/ERR675624/FindFungi/Processing/Consensus.sorted.ERR675624.All-Kraken-Results.tsv /lustre/home/acct-clslzy/clslzy/home/qqsong/myshell/findfungi/test/ERR675624/FindFungi/Results/BLAST_Processing/All-Skewness-Scores Final_Results_ERR675624.tsv > MyScript.log MyScript.log is empty.
0 Jun 15 20:12 Final_Results_ERR675624.tsv 14M Jun 15 20:12 Final_Results_ERR675624.tsv_AllResults.tsv 0 Jun 15 20:12 MyScript.log

GiantSpaceRobot commented 4 years ago

My apologies, I didn't attach the test version of the script. Please email me at pauldonovandonegal@gmail.com and I will reply with the test script. Thank you.

sqqsjc commented 4 years ago

Dear sir/madam, ok. I have sent an email to you. Regadrs

GiantSpaceRobot commented 4 years ago

Apologies for the delay. Ok, it looks like the problem lies with Skewness score generation. All scores outputted were exactly the same (0.688247201612). Can you please send me the following:

Thank you.

sqqsjc commented 4 years ago

Dear Paul, Thank you very much for your reply again. The attachment is BLAST output file: Results/BLAST_Processing/BLAST.1759314 TopHits output file: Results/BLAST_Processing/Top-Hits.BLAST.1759314 Hit distribution file: Results/BLAST_Processing/Hit-Distribution.BLAST.1759314 I hope to hear good news from you! Thank you!

Regards Qian

sqqsjc@sjtu.edu.cn

From: Paul Donovan Date: 2020-06-16 23:50 To: GiantSpaceRobot/FindFungi CC: sqqsjc; Author Subject: Re: [GiantSpaceRobot/FindFungi] issues with Running FindFungi-0.23.3.sh (#13) Apologies for the delay. Ok, it looks like the problem lies with Skewness score generation. All scores outputted were exactly the same (0.688247201612). Can you please send me the following: BLAST output file: Results/BLAST_Processing/BLAST.1759314 TopHits output file: Results/BLAST_Processing/Top-Hits.BLAST.1759314 Hit distribution file: Results/BLAST_Processing/Hit-Distribution.BLAST.1759314 Thank you. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

GiantSpaceRobot commented 4 years ago

Hi Qian, Could you try to send them again as I did not receive them. Thanks, and hopefully I'll have good news for you soon.

Best, Paul

On Tue, Jun 16, 2020 at 5:08 PM sqqsjc notifications@github.com wrote:

Dear Paul, Thank you very much for your reply again. The attachment is BLAST output file: Results/BLAST_Processing/BLAST.1759314 TopHits output file: Results/BLAST_Processing/Top-Hits.BLAST.1759314 Hit distribution file: Results/BLAST_Processing/Hit-Distribution.BLAST.1759314 I hope to hear good news from you! Thank you!

Regards Qian

sqqsjc@sjtu.edu.cn

From: Paul Donovan Date: 2020-06-16 23:50 To: GiantSpaceRobot/FindFungi CC: sqqsjc; Author Subject: Re: [GiantSpaceRobot/FindFungi] issues with Running FindFungi-0.23.3.sh (#13) Apologies for the delay. Ok, it looks like the problem lies with Skewness score generation. All scores outputted were exactly the same (0.688247201612). Can you please send me the following: BLAST output file: Results/BLAST_Processing/BLAST.1759314 TopHits output file: Results/BLAST_Processing/Top-Hits.BLAST.1759314 Hit distribution file: Results/BLAST_Processing/Hit-Distribution.BLAST.1759314 Thank you. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/GiantSpaceRobot/FindFungi/issues/13#issuecomment-644860528, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHUCDTS2IBHTNMHWOU23MTRW6KHBANCNFSM4N4HXWFQ .

sqqsjc commented 4 years ago

Dear Paul, Of course.The attachments are newly transmitted. Thank you!

Regards Qian

sqqsjc@sjtu.edu.cn

From: Paul Donovan Date: 2020-06-17 01:11 To: GiantSpaceRobot/FindFungi CC: sqqsjc; Author Subject: Re: [GiantSpaceRobot/FindFungi] issues with Running FindFungi-0.23.3.sh (#13) Hi Qian, Could you try to send them again as I did not receive them. Thanks, and hopefully I'll have good news for you soon.

Best, Paul

On Tue, Jun 16, 2020 at 5:08 PM sqqsjc notifications@github.com wrote:

Dear Paul, Thank you very much for your reply again. The attachment is BLAST output file: Results/BLAST_Processing/BLAST.1759314 TopHits output file: Results/BLAST_Processing/Top-Hits.BLAST.1759314 Hit distribution file: Results/BLAST_Processing/Hit-Distribution.BLAST.1759314 I hope to hear good news from you! Thank you!

Regards Qian

sqqsjc@sjtu.edu.cn

From: Paul Donovan Date: 2020-06-16 23:50 To: GiantSpaceRobot/FindFungi CC: sqqsjc; Author Subject: Re: [GiantSpaceRobot/FindFungi] issues with Running FindFungi-0.23.3.sh (#13) Apologies for the delay. Ok, it looks like the problem lies with Skewness score generation. All scores outputted were exactly the same (0.688247201612). Can you please send me the following: BLAST output file: Results/BLAST_Processing/BLAST.1759314 TopHits output file: Results/BLAST_Processing/Top-Hits.BLAST.1759314 Hit distribution file: Results/BLAST_Processing/Hit-Distribution.BLAST.1759314 Thank you. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/GiantSpaceRobot/FindFungi/issues/13#issuecomment-644860528, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGHUCDTS2IBHTNMHWOU23MTRW6KHBANCNFSM4N4HXWFQ .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

GiantSpaceRobot commented 4 years ago

The user created a fresh Conda environment and installed the SLURM adaptation of FindFungi here. This worked.

The initial issue remains undiagnosed but appeared to be related to a mismatch with the input and output of BLAST.