I'm trying to run coverm contig with the --sharded flag, but it appears to generate some issues which is difficult to comprehend.
My current command is:
coverm contig -1 ../AAF6d_no_host_R1.fq.gz -2 ../AAF6d_no_host_R2.fq.gz -r ../all_contigs.fa_part00 ../all_contigs.fa_part01 --sharded --bam-file-cache-directory bam_file
/ -m count -o coverage.out -t 4 -v > log4 2>&1
And the log file ends with :
[2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Read records [Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)]
[2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Read records [Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)]
[2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Previous records Some([Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)])
[2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Second read records [Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)]
thread 'main' panicked at src/lib.rs:165:17:
Unexpected data type of AS aux tag, found I8(-4)
stack backtrace:
note: Some details are omitted, run with RUST_BACKTRACE=full for a verbose backtrace.
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
[E::hts_open_format] Failed to open file "/tmp/coverm_fifo.tciRO3QHk3WL/sort_output.pipe" : No such file or directory
samtools sort: failed to create "/tmp/coverm_fifo.tciRO3QHk3WL/sort_output.pipe": No such file or directory
It's just break at this part and I'm really confused.
Any help is much appreciated!
Hi Ben,
I'm trying to run coverm contig with the --sharded flag, but it appears to generate some issues which is difficult to comprehend.
My current command is: coverm contig -1 ../AAF6d_no_host_R1.fq.gz -2 ../AAF6d_no_host_R2.fq.gz -r ../all_contigs.fa_part00 ../all_contigs.fa_part01 --sharded --bam-file-cache-directory bam_file / -m count -o coverage.out -t 4 -v > log4 2>&1
And the log file ends with : [2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Read records [Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)] [2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Read records [Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)] [2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Previous records Some([Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)]) [2024-02-23T09:06:46Z DEBUG coverm::shard_bam_reader] Second read records [Record(tid: 134768, pos: 93), Record(tid: -1, pos: -1)] thread 'main' panicked at src/lib.rs:165:17: Unexpected data type of AS aux tag, found I8(-4) stack backtrace: note: Some details are omitted, run with
RUST_BACKTRACE=fullfor a verbose backtrace. [bam_sort_core] merging from 0 files and 4 in-memory blocks... [E::hts_open_format] Failed to open file "/tmp/coverm_fifo.tciRO3QHk3WL/sort_output.pipe" : No such file or directory samtools sort: failed to create "/tmp/coverm_fifo.tciRO3QHk3WL/sort_output.pipe": No such file or directoryIt's just break at this part and I'm really confused. Any help is much appreciated!