iostream error 4

[yangyxt]

Tried to run dragmap, the commands are:
dragen-os -r /paedyl01/disk1/yangyxt/indexed_genome/hg19 -1 /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/forward_read/TCA-082A-542_1.fastq.gz -2 /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/reverse_read/TCA-082A-542_2.fastq.gz --num-threads 10 --Aligner.sec-aligns 5 --fastq-offset 30 --Aligner.sw-method dragen --verbose --RGID TCA-082A --RGSM TCA-082A --output-directory /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A --output-file-prefix test.bqsr
It ended up with an IO stream error, while the later part of the error log looks like this:
decompHashTableCtxInit... 0.630 seconds decompHashTableHeader... 0.002 seconds decompHashTableLiterals... 0.511 seconds decompHashTableExtIndex... 0.031 seconds decompHashTableAutoHits... 7.618 seconds decompHashTableSetFlags... 1.006 seconds finished decompress INFO: writing SAM file to "/paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/test.bqsr.sam" INFO: writing mapping metrics stats into "/paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/test.bqsr.mapping_metrics.csv" Running fastq workflow on 10 threads. System supports 80 threads. 0 249 0 0 0 0 10000 1 40000 1 1000 0 0 0 6 0 250 0 0 0 0 10000 1 40000 1 1000 0 0 0 5 0 251 0 0 0 0 10000 1 40000 1 1000 0 0 0 4 0 252 0 0 0 0 10000 1 40000 1 1000 0 0 0 3 0 253 0 0 0 0 10000 1 40000 1 1000 0 0 0 2 0 254 0 0 0 0 10000 1 40000 1 1000 0 0 0 1 [46984712248960] ERROR: This thread caught an exception first Error: boost::exception: /opt/conda/conda-bld/dragmap_1659316645256/work/src/lib/workflow/Input2SamWorkflow.cpp(459): Throw in function void dragenos::workflow::parseSingleInput(std::ostream&, const dragenos::options::DragenOsOptions&, const dragenos::reference::ReferenceSequence&, const dragenos::reference::HashtableConfig&, const dragenos::reference::Hashtable&, std::ostream&) Dynamic exception type: boost::wrapexcept<std::runtime_error> std::exception::what: gzip error: iostream error 4

I make sure that reference genome are indexed and are used to built hash table. Also the input forward read and reverse read are valid.

I dunno what's going on. Pls share some insights about the potential cause ? Thanks!

[yangyxt]

I found that the error log is not correctly wrapped so here I provide a screenshot for your convenience:

Thanks!

[famosab]

Was this resolved? I ran into the same error today!