kapsakcj / nanoporeWorkflow

:dna: Shell scripts for working with bacterial isolate Nanopore sequence data on CDC servers
MIT License
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dig into Flye error - CRC check failed #36

Closed kapsakcj closed 3 years ago

kapsakcj commented 3 years ago

Tori encountered this a few times when running flye

$NSLOTS set to: 16
$INDIR is set to: basecalling-2020-23-11/demux/barcode06/
Tue Nov 24 11:52:02 EST 2020
node96.hpc.biotech.cdc.gov
Directory ./flye.1Qfh8Q/log has been created
/opt/sge/default/spool/node96/job_scripts/8747716: temp dir is ./flye.1Qfh8Q
$BARCODE is set to: barcode06
$LENGTHS set to: basecalling-2020-23-11/demux/barcode06/readlengths.txt.gz
Min length for 120 coverage will be 1
Assembling with flye...
WARNING: Could not chdir to home: /scicomp/home/nzu0
[2020-11-24 16:52:05] INFO: Starting Flye 2.7-b1585
[2020-11-24 16:52:05] INFO: >>>STAGE: configure
[2020-11-24 16:52:05] INFO: Configuring run
[2020-11-24 16:52:05] ERROR: CRC check failed 0x20fb0008 != 0x0L
[2020-11-24 16:52:05] ERROR: Pipeline aborted
kapsakcj commented 3 years ago

This happened because the fastq.gz file was pretty much empty. not related to flye at all