Error in unserialize(socklist[[n]]) : error reading from connection

[THZ34]

Hi, I have run the script 'Viral_Track_scanning.R' with the command 'Viral_Track_scanning.R Parameters.txt files_to_process.txt' Content of 'Parameters.txt' is: N_thread=14 Output_directory=/data/active_data/thz/1.16nsfc/lung_sc/virus_express/result/ Index_genome=/data/active_data/thz/1.16nsfc/lung_sc/virus_express/ref_index/ Viral_annotation_file=/data/active_data/thz/1.16nsfc/lung_sc/virus_express/Viral-Track/Virusite_annotation_file.txt Name_run="BALF" Load_STAR_module=FALSE Load_samtools_module=FALSE Load_stringtie_module=FALSE Minimal_read_mapped=50 Single_cell_metadata=/data/active_data/thz/1.16nsfc/lung_sc/virus_express/wells_cells.txt

Content of 'files_to_process.txt' is: /data/active_data/thz/1.16nsfc/lung_sc/virus_express/rawdata/SRR11181958.fastq

However, 'Error in unserialize(socklist[[n]]) : error reading from connection' has happened, The following is the log: Rscript Viral_Track_scanning.R Parameters.txt Files_to_process.txt Loading of the libraries.... Warning messages: 1: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘SummarizedExperiment’ 2: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘ShortRead’ ... done ! 1 Fastq files are going to be processed ! Mapping SRR11181958.fastq file May 22 16:46:54 ..... started STAR run May 22 16:46:54 ..... loading genome May 22 16:47:25 ..... started 1st pass mapping May 22 17:56:05 ..... finished 1st pass mapping May 22 17:56:06 ..... inserting junctions into the genome indices May 22 18:00:11 ..... started mapping May 22 19:24:52 ..... started sorting BAM May 22 21:17:17 ..... finished successfully Mapping ofSRR11181958.fastq done ! All fastq files have been mapped successfully Starting the BAM file analysis Indexing of the bam file for SRR11181958 is done Computing stat file for the bam file for SRR11181958 is done Checking the mapping quality of each virus... Export of the viral SAM file done for SRR11181958 Error in unserialize(socklist[[n]]) : error reading from connection Calls: %dopar% ... recvOneData -> recvOneData.SOCKcluster -> unserialize Execution halted

[polojacky]

Apparently, this error occurs when the master process got an error when calling unserialize to read from one of the workers, i.e., dopar. Can you post the file list under Viral_BAM_files directory? Or you can set N_thread=1 and only run the code from line 335 in Viral_Track_scanning.R. Maybe you can find more details about the error.

[THZ34]

I have tried to set N_thread=1 and only run the code from line 335 in Viral_Track_scanning.R, the error is 'Error in foreach(i = rownames(temp_chromosome_count), .combine = rbind, : could not find function "%dopar%"'

Files in Viral_BAM_files are: chr10.bam chr18_KI270863v1_alt.bam chr2_KI270773v1_alt.bam chr9_KI270718v1_random.bam chr10_GL383545v1_alt.bam chr18_KI270911v1_alt.bam chr2_KI270774v1_alt.bam chr9_KI270719v1_random.bam chr10_GL383546v1_alt.bam chr18_KI270912v1_alt.bam chr2_KI270775v1_alt.bam chr9_KI270720v1_random.bam chr10_KI270824v1_alt.bam chr19.bam chr2_KI270776v1_alt.bam chr9_KI270823v1_alt.bam chr10_KI270825v1_alt.bam chr19_GL383573v1_alt.bam chr2_KI270893v1_alt.bam chrM.bam chr11.bam chr19_GL383574v1_alt.bam chr2_KI270894v1_alt.bam chrUn_GL000195v1.bam chr11_GL383547v1_alt.bam chr19_GL383575v2_alt.bam chr3.bam chrUn_GL000213v1.bam chr11_JH159136v1_alt.bam chr19_GL383576v1_alt.bam chr3_GL000221v1_random.bam chrUn_GL000214v1.bam chr11_JH159137v1_alt.bam chr19_GL949746v1_alt.bam chr3_GL383526v1_alt.bam chrUn_GL000216v2.bam chr11_KI270721v1_random.bam chr19_GL949747v2_alt.bam chr3_JH636055v2_alt.bam chrUn_GL000218v1.bam chr11_KI270826v1_alt.bam chr19_GL949748v2_alt.bam chr3_KI270777v1_alt.bam chrUn_GL000219v1.bam chr11_KI270827v1_alt.bam chr19_GL949749v2_alt.bam chr3_KI270778v1_alt.bam chrUn_GL000220v1.bam chr11_KI270829v1_alt.bam chr19_GL949750v2_alt.bam chr3_KI270779v1_alt.bam chrUn_GL000224v1.bam chr11_KI270830v1_alt.bam chr19_GL949751v2_alt.bam chr3_KI270780v1_alt.bam chrUn_KI270330v1.bam chr11_KI270831v1_alt.bam chr19_GL949752v1_alt.bam chr3_KI270781v1_alt.bam chrUn_KI270435v1.bam chr11_KI270832v1_alt.bam chr19_GL949753v2_alt.bam chr3_KI270782v1_alt.bam chrUn_KI270438v1.bam chr11_KI270902v1_alt.bam chr19_KI270865v1_alt.bam chr3_KI270783v1_alt.bam chrUn_KI270442v1.bam chr11_KI270903v1_alt.bam chr19_KI270866v1_alt.bam chr3_KI270784v1_alt.bam chrUn_KI270448v1.bam chr11_KI270927v1_alt.bam chr19_KI270867v1_alt.bam chr3_KI270895v1_alt.bam chrUn_KI270519v1.bam chr12.bam chr19_KI270868v1_alt.bam chr3_KI270924v1_alt.bam chrUn_KI270538v1.bam chr12_GL383549v1_alt.bam chr19_KI270883v1_alt.bam chr3_KI270934v1_alt.bam chrUn_KI270579v1.bam chr12_GL383550v2_alt.bam chr19_KI270885v1_alt.bam chr3_KI270935v1_alt.bam chrUn_KI270741v1.bam chr12_GL383551v1_alt.bam chr19_KI270887v1_alt.bam chr3_KI270936v1_alt.bam chrUn_KI270742v1.bam chr12_GL383552v1_alt.bam chr19_KI270888v1_alt.bam chr3_KI270937v1_alt.bam chrUn_KI270743v1.bam chr12_GL383553v2_alt.bam chr19_KI270889v1_alt.bam chr4.bam chrUn_KI270744v1.bam chr12_GL877875v1_alt.bam chr19_KI270891v1_alt.bam chr4_GL000008v2_random.bam chrUn_KI270745v1.bam chr12_GL877876v1_alt.bam chr19_KI270914v1_alt.bam chr4_GL000257v2_alt.bam chrUn_KI270746v1.bam chr12_KI270833v1_alt.bam chr19_KI270915v1_alt.bam chr4_GL383527v1_alt.bam chrUn_KI270747v1.bam chr12_KI270834v1_alt.bam chr19_KI270917v1_alt.bam chr4_GL383528v1_alt.bam chrUn_KI270748v1.bam chr12_KI270835v1_alt.bam chr19_KI270919v1_alt.bam chr4_KI270785v1_alt.bam chrUn_KI270749v1.bam chr12_KI270836v1_alt.bam chr19_KI270920v1_alt.bam chr4_KI270786v1_alt.bam chrUn_KI270750v1.bam chr12_KI270837v1_alt.bam chr19_KI270921v1_alt.bam chr4_KI270787v1_alt.bam chrUn_KI270751v1.bam chr12_KI270904v1_alt.bam chr19_KI270922v1_alt.bam chr4_KI270788v1_alt.bam chrUn_KI270753v1.bam chr13.bam chr19_KI270923v1_alt.bam chr4_KI270789v1_alt.bam chrUn_KI270754v1.bam chr13_KI270838v1_alt.bam chr19_KI270929v1_alt.bam chr4_KI270790v1_alt.bam chrUn_KI270755v1.bam chr13_KI270839v1_alt.bam chr19_KI270930v1_alt.bam chr4_KI270896v1_alt.bam chrUn_KI270757v1.bam chr13_KI270840v1_alt.bam chr19_KI270931v1_alt.bam chr4_KI270925v1_alt.bam chrX.bam chr13_KI270841v1_alt.bam chr19_KI270932v1_alt.bam chr5.bam chrX_KI270880v1_alt.bam chr13_KI270842v1_alt.bam chr19_KI270933v1_alt.bam chr5_GL000208v1_random.bam chrX_KI270881v1_alt.bam chr13_KI270843v1_alt.bam chr19_KI270938v1_alt.bam chr5_GL339449v2_alt.bam chrX_KI270913v1_alt.bam chr14.bam chr1.bam chr5_GL383530v1_alt.bam chrY.bam chr14_GL000009v2_random.bam chr1_GL383518v1_alt.bam chr5_GL383531v1_alt.bam chrY_KI270740v1_random.bam chr14_GL000194v1_random.bam chr1_GL383519v1_alt.bam chr5_GL949742v1_alt.bam 'refseq|NC_001479|7835nt|Encephalomyocarditis.bam' chr14_GL000225v1_random.bam chr1_GL383520v2_alt.bam chr5_KI270791v1_alt.bam 'refseq|NC_001782|1801nt|Saccharomyces.bam' chr14_KI270722v1_random.bam chr1_KI270706v1_random.bam chr5_KI270792v1_alt.bam 'refseq|NC_002794|195859nt|Tupaiid.bam' chr14_KI270723v1_random.bam chr1_KI270707v1_random.bam chr5_KI270793v1_alt.bam 'refseq|NC_003988|7374nt|Simian.bam' chr14_KI270725v1_random.bam chr1_KI270708v1_random.bam chr5_KI270794v1_alt.bam 'refseq|NC_004006|2293nt|Broad.bam' chr14_KI270726v1_random.bam chr1_KI270709v1_random.bam chr5_KI270795v1_alt.bam 'refseq|NC_004102|9646nt|Hepatitis.bam' chr14_KI270844v1_alt.bam chr1_KI270711v1_random.bam chr5_KI270796v1_alt.bam 'refseq|NC_004560|5784nt|Oyster.bam' chr14_KI270845v1_alt.bam chr1_KI270712v1_random.bam chr5_KI270897v1_alt.bam 'refseq|NC_004718|29751nt|SARS.bam' chr14_KI270846v1_alt.bam chr1_KI270713v1_random.bam chr5_KI270898v1_alt.bam 'refseq|NC_004812|156789nt|Macacine.bam' chr14_KI270847v1_alt.bam chr1_KI270714v1_random.bam chr6.bam 'refseq|NC_006553|8289nt|Avian.bam' chr15.bam chr1_KI270759v1_alt.bam chr6_GL000250v2_alt.bam 'refseq|NC_007415|5470nt|Sclerotinia.bam' chr15_GL383554v1_alt.bam chr1_KI270760v1_alt.bam chr6_GL000251v2_alt.bam 'refseq|NC_008310|6485nt|Hibiscus.bam' chr15_GL383555v2_alt.bam chr1_KI270761v1_alt.bam chr6_GL000252v2_alt.bam 'refseq|NC_008580|8380nt|Rabbit.bam' chr15_KI270727v1_random.bam chr1_KI270762v1_alt.bam chr6_GL000253v2_alt.bam 'refseq|NC_009448|8115nt|Saffold.bam' chr15_KI270848v1_alt.bam chr1_KI270763v1_alt.bam chr6_GL000254v2_alt.bam 'refseq|NC_009758|8926nt|Marine.bam' chr15_KI270849v1_alt.bam chr1_KI270765v1_alt.bam chr6_GL000255v2_alt.bam 'refseq|NC_009823|9711nt|Hepatitis.bam' chr15_KI270850v1_alt.bam chr1_KI270766v1_alt.bam chr6_GL000256v2_alt.bam 'refseq|NC_009827|9628nt|Hepatitis.bam' chr15_KI270851v1_alt.bam chr1_KI270892v1_alt.bam chr6_GL383533v1_alt.bam 'refseq|NC_013110|2344nt|Primula.bam' chr15_KI270852v1_alt.bam chr20.bam chr6_KB021644v2_alt.bam 'refseq|NC_013220|3220nt|Phytophthora.bam' chr15_KI270905v1_alt.bam chr20_GL383577v2_alt.bam chr6_KI270758v1_alt.bam 'refseq|NC_013221|2896nt|Phytophthora.bam' chr15_KI270906v1_alt.bam chr20_KI270869v1_alt.bam chr6_KI270797v1_alt.bam 'refseq|NC_015874|20192nt|Nam.bam' chr16.bam chr20_KI270870v1_alt.bam chr6_KI270798v1_alt.bam 'refseq|NC_020100|2796nt|Aspergillus.bam' chr16_GL383556v1_alt.bam chr21.bam chr6_KI270799v1_alt.bam 'refseq|NC_020235|1828nt|Rosellinia.bam' chr16_GL383557v1_alt.bam chr21_GL383578v2_alt.bam chr6_KI270800v1_alt.bam 'refseq|NC_021095|2348nt|White.bam' chr16_KI270728v1_random.bam chr21_GL383579v2_alt.bam chr6_KI270801v1_alt.bam 'refseq|NC_021097|2353nt|Red.bam' chr16_KI270853v1_alt.bam chr21_GL383580v2_alt.bam chr6_KI270802v1_alt.bam 'refseq|NC_021099|2349nt|Hop.bam' chr16_KI270854v1_alt.bam chr21_GL383581v2_alt.bam chr7.bam 'refseq|NC_021148|2354nt|Dill.bam' chr16_KI270855v1_alt.bam chr21_KI270872v1_alt.bam chr7_GL383534v2_alt.bam 'refseq|NC_022518|9472nt|Human.bam' chr16_KI270856v1_alt.bam chr21_KI270873v1_alt.bam chr7_KI270803v1_alt.bam 'refseq|NC_022615|1837nt|Dill.bam' chr17.bam chr21_KI270874v1_alt.bam chr7_KI270804v1_alt.bam 'refseq|NC_023162|7697nt|Carp.bam' chr17_GL000205v2_random.bam chr22.bam chr7_KI270805v1_alt.bam 'refseq|NC_024112|2847nt|Jingmen.bam' chr17_GL000258v2_alt.bam chr22_GL383582v2_alt.bam chr7_KI270806v1_alt.bam 'refseq|NC_024502|3869nt|Gentian.bam' chr17_GL383563v3_alt.bam chr22_GL383583v2_alt.bam chr7_KI270807v1_alt.bam 'refseq|NC_024709|33452nt|Ball.bam' chr17_GL383564v2_alt.bam chr22_KB663609v1_alt.bam chr7_KI270808v1_alt.bam 'refseq|NC_028094|473558nt|Chrysochromulina.bam' chr17_GL383565v1_alt.bam chr22_KI270731v1_random.bam chr7_KI270809v1_alt.bam 'refseq|NC_028095|1705nt|Torulaspora.bam' chr17_GL383566v1_alt.bam chr22_KI270732v1_random.bam chr7_KI270899v1_alt.bam 'refseq|NC_028250|2499nt|Rosellinia.bam' chr17_JH159146v1_alt.bam chr22_KI270733v1_random.bam chr8.bam 'refseq|NC_029035|3164nt|Colombian.bam' chr17_JH159147v1_alt.bam chr22_KI270734v1_random.bam chr8_KI270810v1_alt.bam 'refseq|NC_029302|6038nt|Piscine.bam' chr17_JH159148v1_alt.bam chr22_KI270735v1_random.bam chr8_KI270811v1_alt.bam 'refseq|NC_031032|24320nt|Bacillus.bam' chr17_KI270729v1_random.bam chr22_KI270736v1_random.bam chr8_KI270812v1_alt.bam 'refseq|NC_031338|10056nt|Moku.bam' chr17_KI270730v1_random.bam chr22_KI270737v1_random.bam chr8_KI270813v1_alt.bam 'refseq|NC_032104|7599nt|Arachis.bam' chr17_KI270857v1_alt.bam chr22_KI270738v1_random.bam chr8_KI270814v1_alt.bam 'refseq|NC_036600|2374nt|Rosellinia.bam' chr17_KI270858v1_alt.bam chr22_KI270875v1_alt.bam chr8_KI270815v1_alt.bam 'refseq|NC_037665|1838258nt|Pandoravirus.bam' chr17_KI270859v1_alt.bam chr22_KI270876v1_alt.bam chr8_KI270816v1_alt.bam 'refseq|NC_038425|9531nt|Non-primate.bam' chr17_KI270860v1_alt.bam chr22_KI270877v1_alt.bam chr8_KI270817v1_alt.bam 'refseq|NC_038828|1866nt|Heterobasidion.bam' chr17_KI270861v1_alt.bam chr22_KI270878v1_alt.bam chr8_KI270818v1_alt.bam 'refseq|NC_038838|2354nt|Crimson.bam' chr17_KI270862v1_alt.bam chr22_KI270879v1_alt.bam chr8_KI270819v1_alt.bam 'refseq|NC_040361|41178nt|Planarian.bam' chr17_KI270907v1_alt.bam chr22_KI270928v1_alt.bam chr8_KI270821v1_alt.bam 'refseq|NC_040534|20949nt|Yichang.bam' chr17_KI270908v1_alt.bam chr2.bam chr8_KI270822v1_alt.bam 'refseq|NC_040589|11413nt|Diatom.bam' chr17_KI270909v1_alt.bam chr2_GL383521v1_alt.bam chr8_KI270900v1_alt.bam 'refseq|NC_040615|166748nt|Eptesicus.bam' chr17_KI270910v1_alt.bam chr2_GL383522v1_alt.bam chr8_KI270901v1_alt.bam 'refseq|NC_041925|54836nt|Proteus.bam' chr18.bam chr2_GL582966v2_alt.bam chr8_KI270926v1_alt.bam 'refseq|NC_042057|42925nt|Enterobacteria.bam' chr18_GL383567v1_alt.bam chr2_KI270767v1_alt.bam chr9.bam 'refseq|NC_043054|137452nt|Bubaline.bam' chr18_GL383568v1_alt.bam chr2_KI270768v1_alt.bam chr9_GL383539v1_alt.bam 'refseq|NC_043566|1034nt|Anhembi.bam' chr18_GL383569v1_alt.bam chr2_KI270769v1_alt.bam chr9_GL383540v1_alt.bam 'refseq|NC_043569|998nt|Iaco.bam' chr18_GL383570v1_alt.bam chr2_KI270770v1_alt.bam chr9_GL383541v1_alt.bam 'refseq|NC_043574|1016nt|Cachoeira.bam' chr18_GL383571v1_alt.bam chr2_KI270771v1_alt.bam chr9_GL383542v1_alt.bam 'refseq|NC_045512|29903nt|Severe.bam' chr18_GL383572v1_alt.bam chr2_KI270772v1_alt.bam chr9_KI270717v1_random.bam

[PierreBSC]

This is really weird. What is the platform you are using ? If it is a Windows platform then the parallelisation will probably not work !

[polojacky]

Yes, it's wired. I recommend you remove the parallelization and try for loop in your code. for(i in rownames(temp_chromosome_count)) { } You can store the QC_temp result into a matrix.

BTW, what's the human reference in your analysis. Bam files of host reference are removed in the following analysis (Line 284), but I see chr10.bam chr18_KI270863v1_alt.bam etc in your Viral_BAM_files directory.

[THZ34]

This is really weird. What is the platform you are using ? If it is a Windows platform then the parallelisation will probably not work !

The platform is Ubuntu16.04 with R3.6.3.

[THZ34]

Yes, it's wired. I recommend you remove the parallelization and try for loop in your code. for(i in rownames(temp_chromosome_count)) { } You can store the QC_temp result into a matrix.

BTW, what's the human reference in your analysis. Bam files of host reference are removed in the following analysis (Line 284), but I see chr10.bam chr18_KI270863v1_alt.bam etc in your Viral_BAM_files directory.

Thanks for your advice, I will try it. The reference is hg19, Should I change it to hg38?