corrupted size vs. prev_size

[nick-youngblut]

I'm using quay.io/biocontainers/falco:1.2.2--hdcf5f25_0. The run output:

[limits]	using file /usr/local/opt/falco/Configuration/limits.txt
[adapters]	using file /usr/local/opt/falco/Configuration/adapter_list.txt
[contaminants]	using file /usr/local/opt/falco/Configuration/contaminant_list.txt
[Mon Apr 29 18:30:02 2024] Started reading file 20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001.fastq.gz
[Mon Apr 29 18:30:02 2024] reading file as gzipped FASTQ format
[running falco|                                                   |  0%]corrupted size vs. prev_size
/home/nickyoungblut/tmp/auto-demux/work/20240426_SspArc0132/33/42662ba1c885c4ddfbc2724221e894/.command.sh: line 9:    36 Aborted                 (core dumped) falco 20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001.fastq.gz -D 20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001/fastqc_data.txt -R 20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001/fastqc_report.html -S 20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001/summary.txt
(nextflow)

seqkit stats -a -T 20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001.fastq.gz produces the following output:

file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	N50_num	Q20(%)	Q30(%)	AvgQual	GC(%)
20241218_Parse_CRISPR_K562_cas12a_Sub1_R1_001.fastq.gz	FASTQ	DNA	24322546	12501788644	514	514.0	514	514.0	514.0	514.0	0	514	1	44.39	29.94	11.99	42.50

...so it appears that there is nothing wrong with the fastq file. Note the long read lengths. The RunInfo.xml for this Illumina run was skewed to long Read 1 lengths:

    <Reads>
      <Read NumCycles="514" Number="1" IsIndexedRead="N" />
      <Read NumCycles="86" Number="2" IsIndexedRead="N" />
    </Reads>

[andrewdavidsmith]

@nick-youngblut any chance you can reproduce with a smaller file that can be linked? If not, can you try it with the file unzipped?