HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
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Error was 'No such file or directory' and return code '256' #169

Open MAXINELSX opened 2 years ago

MAXINELSX commented 2 years ago

hi; so sorry to bother you my code is: phyloFlash.pl -lib phyloFlash_db -almosteverything -read1 ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_1.fastq -read2 ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_2.fastq -readlength 150

and the error is [08:51:18] running subcommand: /home/lishuxian/anaconda3/envs/pf/bin/bbmap.sh fast=t minidentity=0.7 -Xmx20g reads=-1 threads=40 po=f outputunmapped=f path=/home/lishuxian/138.1 out=phyloFlash_db.bbmap.sam outm=phyloFlash_db.ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_1.fastq.SSU.1.fq noheader=t ambiguous=all build=1 in=ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_1.fastq bhist=phyloFlash_db.basecompositionhistogram ihist=phyloFlash_db.inserthistogram idhist=phyloFlash_db.idhistogram scafstats=phyloFlash_db.hitstats overwrite=t outm2=phyloFlash_db.ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_1.fastq.SSU.2.fq pairlen=1200 in2=ST2019_10_8_FDME220033526-1r_HNJLMDSX2_L2_clean_2.fastq 2>phyloFlash_db.bbmap.out [09:01:19] FATAL: Tool execution failed!. Error was 'No such file or directory' and return code '256' Check error log file phyloFlash_db.bbmap.out Aborting. [09:01:19] Saving log to file phyloFlash_log_on_error I used this phyloFlash for over 150 samples, and only one sample showed this error, but my other data pretreatments and other analysis are the same and didn't show an error. I checked the https://github.com/HRGV/phyloFlash/issues/95 Though the error code is the same, the reasons are not the same

Xijiao000 commented 9 months ago

yes, the same error occurred in my work, how did you solve it? looking forward to your reply!

Xijiao000 commented 9 months ago

I've solved this problem, mainly because the fastq file had errors in the compression and I recompressed it then it run fine.