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ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes
GNU General Public License v3.0
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error with --short_reads #226

Closed ESWRKJ closed 1 year ago

ESWRKJ commented 1 year ago

Hi, when I run python /public/home/FLNC/SQANTI3/sqanti3_qc.py ../Gh_filter_remove.gtf /public/home/Ghirsutum_gene.gtf /public/home/Ghirsutum_genome.fasta --short_reads short_reads.fofn --saturation --cpus 40 Reported this error "EXITING: because of fatal INPUT file error: could not open read file: /public/home/Iowa/SR/TM_1/SRR1695173_1.fastq.gz /public/home/SR/TM_1/SRR1695173_2.fastq.gz SOLUTION: check that this file exists and has read permision" but I input file all exist and have permission. Why?

aarzalluz commented 1 year ago

@ESWRKJ -could you try supplying decompressed files (.fastq instead of .fastq.gz) and see if the error persists?

ESWRKJ commented 1 year ago

ok I have a try

ESWRKJ commented 1 year ago

there is new error, EXITING because of FATAL ERROR: could not open genome file /public/home/Iowa/SRR14415009/FL/FLNC/map/collapse/2+3/STAR_index//genomeParameters.txt SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

aarzalluz commented 1 year ago

@ESWRKJ the error is thrown by STAR, and it is caused by the paths of the files not being correctly defined in your input command. There is more info in this thread.

Please, verify that the file paths are correct relative to the directory in which you are running SQANTI3. Also, I recommend that you set the output directory using the -d argument to have more control over where the output files are created.