[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.
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.