lucapinello
commented
7 years ago Hi Steve, Yes the problem is that your fastq file is either truncated or malformed (the quality string for one read is shorter than the read itself).
Closed steve-shan closed 7 years ago
lucapinello
commented
7 years ago Hi Steve, Yes the problem is that your fastq file is either truncated or malformed (the quality string for one read is shorter than the read itself).
Hello,
I was trying to use CRISPRessoPoll on my sequence file but received some FLASH error. The following is the log:
`[Command used]: CRISPRessoPooled /Library/Frameworks/Python.framework/Versions/2.7/bin/CRISPRessoPooled -r1 FGC1478_s_1_1_AGGCAGAA-ACTGCATA.fastq.gz -r2 FGC1478_s_1_2_AGGCAGAA-ACTGCATA.fastq.gz -f CRISPResso1111.xlsx
[Execution log]: Merging paired sequences with Flash... [FLASH] Starting FLASH v1.2.11 [FLASH] Fast Length Adjustment of SHort reads [FLASH]
[FLASH] Input files: [FLASH] FGC1478_s_1_1_AGGCAGAA-ACTGCATA.fastq.gz [FLASH] FGC1478_s_1_2_AGGCAGAA-ACTGCATA.fastq.gz [FLASH]
[FLASH] Output files: [FLASH] CRISPRessoPooled_on_FGC1478_s_1_1_AGGCAGAA-ACTGCATA_FGC1478_s_1_2_AGGCAGAA-ACTGCATA/out.extendedFrags.fastq.gz [FLASH] CRISPRessoPooled_on_FGC1478_s_1_1_AGGCAGAA-ACTGCATA_FGC1478_s_1_2_AGGCAGAA-ACTGCATA/out.notCombined_1.fastq.gz [FLASH] CRISPRessoPooled_on_FGC1478_s_1_1_AGGCAGAA-ACTGCATA_FGC1478_s_1_2_AGGCAGAA-ACTGCATA/out.notCombined_2.fastq.gz [FLASH] CRISPRessoPooled_on_FGC1478_s_1_1_AGGCAGAA-ACTGCATA_FGC1478_s_1_2_AGGCAGAA-ACTGCATA/out.hist [FLASH] CRISPRessoPooled_on_FGC1478_s_1_1_AGGCAGAA-ACTGCATA_FGC1478_s_1_2_AGGCAGAA-ACTGCATA/out.histogram [FLASH]
[FLASH] Parameters: [FLASH] Min overlap: 4 [FLASH] Max overlap: 100 [FLASH] Max mismatch density: 0.250000 [FLASH] Allow "outie" pairs: false [FLASH] Cap mismatch quals: false [FLASH] Combiner threads: 8 [FLASH] Input format: FASTQ, phred_offset=33 [FLASH] Output format: FASTQ, phred_offset=33, gzip [FLASH]
[FLASH] Starting reader and writer threads [FLASH] Starting 8 combiner threads [FLASH] Processed 25000 read pairs [FLASH] Processed 50000 read pairs [FLASH] Processed 75000 read pairs [FLASH] Processed 100000 read pairs [FLASH] Processed 125000 read pairs [FLASH] Processed 150000 read pairs [FLASH] Processed 175000 read pairs [FLASH] Processed 200000 read pairs [FLASH] Processed 225000 read pairs [FLASH] Processed 250000 read pairs [FLASH] Processed 275000 read pairs [FLASH] Processed 300000 read pairs [FLASH] Processed 325000 read pairs [FLASH] Processed 350000 read pairs [FLASH] Processed 375000 read pairs [FLASH] ERROR: Qual string length (55) not the same as sequence length (250) (file "FGC1478_s_1_1_AGGCAGAA-ACTGCATA.fastq.gz", near line 1502597) [FLASH] FLASH did not complete successfully; exiting with failure status (1)
ERROR: Flash failed to run, please check the log file. `
It seems like there's something wrong with my fastq file because I can run your test example without any problem, although that did not require CRISPRessoPoll.