BUG Samtools related bug inDrops v3 samples

[droplet-lab]

Describe the bug I get a samtools error when running one of my samples, but it is fine for the other samples, any ideas where this could come from ?

I have tried a few things but nothing has been successful so far. Any help would greatly be appreciated :). Thanks a lot

Warning message: In data.table::fread(cmd = paste(samtools, "view", filtered_bams[1], : File '/tmp/RtmpQBqt4O/file59e963125f9c' has size 0. Returning a NULL data.table. Usage: samtools cat [options] [... ] samtools cat [options] [... ]

Concatenate BAM or CRAM files, first those in , then those on the command line.

Options: -b FILE list of input BAM/CRAM file names, one per line -h FILE copy the header from FILE [default is 1st input file] -o FILE output BAM/CRAM Usage: samtools cat [options] [... ] samtools cat [options] [... ]

Concatenate BAM or CRAM files, first those in , then those on the command line.

Options: -b FILE list of input BAM/CRAM file names, one per line -h FILE copy the header from FILE [default is 1st input file] -o FILE output BAM/CRAM rm: cannot remove '/PATH/tmp.SAMPLE.*': No such file or directory Warning message: In system(paste(STAR_command, "&", sammerge_command, "& wait")) : error in running command Error in gsub("SN:", "", chr) : object 'chr' not found Calls: .makeSAF ... .chromLengthFilter -> [ -> [.data.table -> eval -> eval -> gsub In addition: Warning message: In data.table::fread(bread, col.names = c("chr", "len"), header = F) : File '/tmp/RtmpcLgHAv/file5a4e6ca5199c' has size 0. Returning a NULL data.table. Execution halted Loading required package: yaml Loading required package: Matrix Error in gzfile(file, "rb") : cannot open the connection Calls: rds_to_loom -> readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/PATH/Sample.dgecounts.rds', probable reason 'No such file or directory' Execution halted [E::hts_open_format] Failed to open file NA samtools view: failed to open "NA" for reading: No such file or directory Error in gzfile(file, "rb") : cannot open the connection Calls: readRDS -> gzfile In addition: Warning message: In gzfile(file, "rb") : cannot open compressed file '/PATH/Sample.dgecounts.rds', probable reason 'No such file or directory' Execution halted

To Reproduce project:SAMPLE sequence_files: file1: name: /PATH/SAMPLE_R1.fastq.gz base_definition: cDNA(1-61) file2: name: /PATH/SAMPLE_R2.fastq.gz base_definition: BC(1-8) file3: name: /PATH/SAMPLE_R3.fastq.gz base_definition: BC(1-8) file4: name: /PATH/SAMPLE_R4.fastq.gz base_definition:

• BC(1-8)
• UMI(9-14) reference: STAR_index: /PATH/STAR_HS99 GTF_file: /PATH/Homo_sapiens.GRCh38.99.gtf additional_STAR_params: '' additional_files: ~ out_dir: /PATH/SAMPLE num_threads: 8 mem_limit: 20 filter_cutoffs: BC_filter: num_bases: 3 phred: 20 UMI_filter: num_bases: 1 phred: 20 barcodes: barcode_num: ~ barcode_file: ~ automatic: yes BarcodeBinning: 0 nReadsperCell: 100 counting_opts: introns: yes downsampling: '5000,10000,15000,20000,25000,50000' strand: 1 Ham_Dist: 0 velocyto: yes primaryHit: no twoPass: yes make_stats: yes which_Stage: Filtering zUMIs_directory: /PATH/zUMIs read_layout: PE samtools_exec: samtools pigz_exec: pigz STAR_exec: STAR Rscript_exec: Rscript

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[droplet-lab]

Looks like it was another issue with my environment, re-installing everything seems to run.

Sorry about this