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PierreBSC / Viral-Track

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Error when run viral_Track_scanning.R #21

Closed loubean4073 closed 2 years ago

loubean4073 commented 2 years ago

Hi I met a problem when I ran viral_Track_scanning.R. Here is my log below.

Loading of the libraries.... ... done ! Warning message: Output directory does not exist ! Creating it ! 1 Fastq files are going to be processed ! Mapping 2022210_Taylor_5-V2_Gex2_S2_R2_001.fastq file Mar 03 09:21:12 ..... started STAR run Mar 03 09:21:13 ..... loading genome Mar 03 09:23:34 ..... started 1st pass mapping Mar 03 09:41:57 ..... finished 1st pass mapping Mar 03 09:41:57 ..... inserting junctions into the genome indices Mar 03 09:44:30 ..... started mapping Mar 03 10:10:58 ..... started sorting BAM Mar 03 10:31:24 ..... finished successfully Mapping of2022210_Taylor_5-V2_Gex2_S2_R2_001.fastq done ! All fastq files have been mapped successfully Starting the BAM file analysis Indexing of the bam file for 2022210_Taylor_5-V2_Gex2_S2_R2_001 is done Computing stat file for the bam file for 2022210_Taylor_5-V2_Gex2_S2_R2_001 is done Checking the mapping quality of each virus... Export of the viral SAM file done for 2022210_Taylor_5-V2_Gex2_S2_R2_001 Error in unserialize(socklist[[n]]) : error reading from connection Calls: %dopar% ... recvOneData -> recvOneData.SOCKcluster -> unserialize Execution halted

Is this a problem of lack of RAM? Thank you

PierreBSC commented 2 years ago

Hi,

Sorry for my late reply. This is not problem of RAM but rather a problem with the name of the host chromosome. This was already discussed and solved here : https://github.com/PierreBSC/Viral-Track/issues/17

Best

Pierre

loubean4073 commented 2 years ago

Thank you so much!