From f9ca2ed8453df66fe766df7addcb8085a75d8fdf Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Thu, 30 Nov 2023 23:08:32 +0100 Subject: [PATCH 1/2] [FIX] fasta transformer for trembl entries --- FastOMA/transformer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/FastOMA/transformer.py b/FastOMA/transformer.py index f5e588b..8e7aede 100644 --- a/FastOMA/transformer.py +++ b/FastOMA/transformer.py @@ -16,7 +16,7 @@ def transform(self, header): class ExtractUniProtAccessionFastaHeaderTransformer(FastaHeaderTransformer): def __init__(self): - self._up_re = re.compile(r"[spup]{2}\|(?P[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})\|.*") + self._up_re = re.compile(r"[sptr]{2}\|(?P[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})\|.*") def transform(self, header): m = self._up_re.match(header) From 05a0db3a936385a695cfd8f7cf59eeebdd6d7966 Mon Sep 17 00:00:00 2001 From: Adrian Altenhoff Date: Fri, 1 Dec 2023 11:13:05 +0100 Subject: [PATCH 2/2] fix retry --- conf/base.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/base.config b/conf/base.config index c92b610..18d7b1c 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,9 +15,9 @@ process { time = { check_max( 4.h * task.attempt, 'time' ) } shell = ['/bin/bash', '-euo', 'pipefail'] - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' + //errorStrategy = { task.exitStatus in (130..145) ? 'retry' : 'finish' } + errorStrategy = 'retry' + maxRetries = 3 withLabel:process_single { cpus = { check_max( 1 , 'cpus' ) }