operational failures

[maocheng2020]

There was an error when I run the following command,

coverm genome \ -1 /root/data/69_cleandata_1 -2 /root/data69_cleandata_2 \ --genome-fasta-directory /root/data/bin -o output.tsv \ --min-read-percent-identity 0.95 --min-read-aligned-percent 0.75 --trim-min 0.10 --trim-max 0.90 --threads 60

(coverm) root@61940ad43f0a:~/data/coverm# [2022-02-21T14:25:29Z INFO coverm] CoverM version 0.6.1 [2022-02-21T14:25:29Z INFO coverm] Writing output to file: output.tsv [2022-02-21T14:25:29Z INFO coverm] Using min-covered-fraction 10% [2022-02-21T14:25:29Z INFO coverm] Using min-read-percent-identity 95% [2022-02-21T14:25:29Z INFO coverm] Using min-read-aligned-percent 75% [2022-02-21T14:25:29Z INFO bird_tool_utils::external_command_checker] Found minimap2 version 2.17-r941 [2022-02-21T14:25:29Z INFO bird_tool_utils::external_command_checker] Found samtools version 1.14 [2022-02-21T14:25:29Z INFO coverm] Profiling 188 genomes [2022-02-21T14:25:29Z INFO coverm] Generating concatenated reference FASTA file of 188 genomes .. [2022-02-21T14:25:30Z INFO coverm] Not pre-generating minimap2 index [2022-02-21T14:25:52Z WARN coverm::genome] No primary alignments were observed for sample 69_cleandata_1 - perhaps something went wrong in the mapping? [2022-02-21T14:25:52Z INFO coverm::genome] In sample '69_cleandata_1', found 0 reads mapped out of 0 total (NaN%) thread 'main' panicked at 'index out of bounds: the len is 0 but the index is 0', src/coverage_printer.rs:467:35 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

thanks!

[wwood]

Hi,

My suspicion here is that /root/data/69_cleandata_1 and/or /root/data/69_cleandata_2 are not correctly formatted fasta, fastq or gzipped fasta/fastq e.g. that they are empty.

Am I off base?

[SebasSaenz]

Hi,

I was having this issue and it took me a few minutes to solve it. I misspeled the path pointing to the reads. So if you are having this error, it probably means that the files can not be found. So maybe check your paths and file names.

Cheers

[wwood]

Thanks @SebasSaenz for sharing. Ideally CoverM would give a more useful error in that case, so I'll leave this issue open.

[maocheng2020]

Thank you for your kind help.@SebasSaenz@wwood

[wwood]

Hi, I think this is fixed now - the minimap2 error says the file not found, so closing.