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DrosophilaGenomeEvolution / TrEMOLO

Transposable Elements MOvement detection using LOng reads
GNU General Public License v3.0
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/usr/bin/bash: line 196: kill: (1156106) - No such process #15

Closed CrayonLinchan closed 6 months ago

CrayonLinchan commented 6 months ago

Hello, Firstly, I want to express my gratitude for providing such a remarkable tool!!! I have been experimenting with TrEMOLO (Insider) on two Arabidopsis thaliana genome assemblies and encountered an issue while identifying TSD. The installation was successful, as evidenced by a successful test run. However, during the actual run, I encountered the following error: Building a new DB, current time: 12/11/2023 17:09:36 New DB name: /test/TrEMOLO_OUTPUT/INPUT/PSEUDO_panEDTA.TElib.fasta New DB title: /test/TrEMOLO_OUTPUT/INPUT/PSEUDO_panEDTA.TElib.fasta Sequence type: Nucleotide Deleted existing Nucleotide BLAST database named /test/TrEMOLO_OUTPUT/INPUT/PSEUDO_panEDTA.TElib.fasta Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 780 sequences in 0.0204461 seconds. BYE ! AN ERROR OCCURRED! [SNK INFO] ERROR PIPELINE; snakefile used : /test/TrEMOLO_OUTPUT/SNAKE_USED/Snakefile_insider.snk snake log file : /test/TrEMOLO_OUTPUT/log/Snakefile_insider.log Error file : /test/TrEMOLO_OUTPUT/log/Snakefile_insider.err /usr/bin/bash: line 196: kill: (1156106) - No such process Moreover, the detailed error information in Snakefile_insider.err is as follows: FASTA-Reader: Ignoring invalid residues at position(s): On line 11898: 38 /usr/bin/bash: line 191: count_task_running: unbound variable [Mon Dec 11 10:48:37 2023] Error in rule TSD_MULTI_THREADS: jobid: 2 output: /test/TrEMOLO_OUTPUT/VALUES_TSD_INSIDER_GROUP.csv, /test/TrEMOLO_OUTPUT/tmp_TrEMOLO_output_rule/rule_tmp_TSD_MULTI_THREADS_TrEMOLO_OUTPUT log: /test/TrEMOLO_OUTPUT/log/TSD (check log file(s) for error message)

I have been unable to identify the root cause of this problem. I would be happy to provide additional details to help resolve the issue. Best regards

M-D75 commented 6 months ago

Hello,

Thank you for reporting this bug. It was an issue related to an empty variable when only the INSIDER module is used.

The problem has now been fixed. An update is available, you can retrieve it with git pull or do a new git clone ...

If the problem persists or if you encounter any other issues, please do not hesitate to let us know.

Also, please note that another update will be available soon. It will introduce a new way to identify TSD more reliably and much faster.

Thank you. M-D

CrayonLinchan commented 6 months ago

Hello,

I wanted to express my sincere thanks for fixing this bug. With this updates, I reran the program successfully. I appreciate your quick and effective support. Looking forward to the upcoming update with the new TSD identification method. Thanks for the heads up!!

Best regards :)

M-D75 commented 6 months ago

Hello,

I have received the email with a summary of the issue you identified. I hope you are no longer experiencing this problem, but I thank you for bringing it to our attention. The resolution of this issue will be carried out during the upcoming updates.

Thank you, M-D