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How to manually input PHRED score (Err 255) #562

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goforth-familia opened this issue Nov 21, 2024 · 0 comments
Open

How to manually input PHRED score (Err 255) #562

goforth-familia opened this issue Nov 21, 2024 · 0 comments

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@goforth-familia
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I am trying to run the metaWRAP assembly module, but I get an error message that says that PHRED score could not be detected and to manually input it. The problem is I am not sure how to manually input it in the assembly module.

This is the command I ran:
metawrap assembly -1 concat_clean_202A/CLEAN_READS_1-77_1.fastq -2 concat_clean_202A/CLEAN_READS_1-77_2.fastq -m 200 -t 48 --metaspades -o ASSEMBLY

This is part of the error message I received:
== Running read error correction tool: /metawrap/share/spades-3.10.1-1/bin/hammer
0:00:00.000 4M / 4M INFO General (main.cpp : 83) Starting BayesHammer, built from N/A, git re$ 0:00:00.000 4M / 4M INFO General (main.cpp : 84) Loading config from /data/biol-micro-genomic$
0:00:00.001 4M / 4M INFO General (memory_limit.hpp : 47) Memory limit set to 200 Gb
0:00:00.001 4M / 4M INFO General (main.cpp : 93) Trying to determine PHRED offset
0:00:00.002 4M / 4M ERROR General (main.cpp : 96) Failed to determine offset! Specify it manually and restart, please!

== Error == system call for: /metawrap/share/spades-3.10.1-1/bin/hammer', '/ASSEMBLY/metaspades/corrected/configs/config.info']" finished abnormally, err code: 255

Any help is much appreciated to figure out how to add the PHRED score manually. Or unless there is a different error, if you could help me understand it, I appreciate it.
Thank you!

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