phyloFlash
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Error was 'No such file or directory' and return code '256'
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
yes, the same error occurred in my work, how did you solve it? looking forward to your reply!
I've solved this problem, mainly because the fastq file had errors in the compression and I recompressed it then it run fine.