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wwood / CoverM

Read coverage calculator for metagenomics
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Failed to correctly find or parse BAM file at "/tmp/coverm_fifo.tDWtDjcZrfy4/foo.pipe" #127

Open Hollyhlp opened 2 years ago

Hollyhlp commented 2 years ago

Hello, I was using coverm to calculate the reads count mapped to a few genomes. But i frequently met the following probelm. Would you please help me to take a look? Thank you.

(coverm) user@user-X11DPi-N-T:/data3/HLP$ coverm genome --coupled /data3/QITA/lp/D2/WWTP_DNA/BLG_8/READ_QC/BLG0/final_pure_reads_1.fastq /data3/QITA/lp/D2/WWTP_DNA/BLG_8/READ_QC/BLG0/final_pure_reads_2.fastq --genome-fasta-directory /data3/HLP/srenamed/ -o BLG-DNA-abundance/BLG0-count -p bwa-mem -t 5 --min-read-aligned-percent 0.75 --min-read-percent-identity 0.95 --min-covered-fraction 0 -m count [2022-08-03T01:26:50Z INFO coverm] CoverM version 0.6.1 [2022-08-03T01:26:50Z INFO coverm] Writing output to file: BLG-DNA-abundance/BLG0-count [2022-08-03T01:26:50Z INFO coverm] Using min-covered-fraction 0% [2022-08-03T01:26:50Z INFO coverm] Using min-read-percent-identity 95% [2022-08-03T01:26:50Z INFO coverm] Using min-read-aligned-percent 75% [2022-08-03T01:26:50Z INFO bird_tool_utils::external_command_checker] Found samtools version 1.15.1 [2022-08-03T01:26:50Z INFO coverm] Profiling 8 genomes [2022-08-03T01:26:50Z INFO coverm] Generating concatenated reference FASTA file of 8 genomes .. [2022-08-03T01:26:50Z INFO coverm::mapping_index_maintenance] Generating BWA_MEM index for /tmp/.tmp36rBCq .. [2022-08-03T01:26:52Z INFO coverm::mapping_index_maintenance] Finished generating BWA_MEM index. [2022-08-03T01:26:52Z ERROR coverm::bam_generator] Failed to correctly find or parse BAM file at "/tmp/coverm_fifo.tDWtDjcZrfy4/foo.pipe": unable to open SAM/BAM/CRAM file at /tmp/coverm_fifo.tDWtDjcZrfy4/foo.pipe [2022-08-03T01:26:52Z ERROR coverm::bam_generator] Error when running mapping process. Exitstatus was ExitStatus(unix_wait_status(256)). Command run was: ["bash -c \"set -e -o pipefail; bwa mem -t 5 '/tmp/coverm-mapping-index.WD0CYBtMrBNV/.tmp36rBCq' '/data3/QITA/lp/D2/WWTP_DNA/BLG_8/READ_QC/BLG0/final_pure_reads_1.fastq' '/data3/QITA/lp/D2/WWTP_DNA/BLG_8/READ_QC/BLG0/final_pure_reads_2.fastq' 2>/tmp/.tmpbyEVvJ | samtools sort -T '/tmp/coverm_fifo.tDWtDjcZrfy4/coverm-make-samtools-sort3lUFw7' -l0 -@ 4 2>/tmp/.tmphqmAVn > \"/tmp/coverm_fifo.tDWtDjcZrfy4/foo.pipe\"\""] [2022-08-03T01:26:52Z ERROR coverm::bam_generator] The STDERR for the BWA_MEM part was: [bns_restore_core] Error reading /tmp/coverm-mapping-index.WD0CYBtMrBNV/.tmp36rBCq.amb : Unexpected end of file

[2022-08-03T01:26:52Z ERROR coverm::bam_generator] The STDERR for the samtools sort part was: samtools sort: failed to read header from "-"

[2022-08-03T01:26:52Z ERROR coverm::bam_generator] Cannot continue since mapping failed. (coverm) user@user-X11DPi-N-T:/data3/HLP$

faylward commented 1 year ago

I got this error when I didn't have enough RAM. Once I moved to a more powerful machine it worked.