[FLASH] Starting FLASH v1.2.11
[FLASH] Fast Length Adjustment of SHort reads
[FLASH]  
[FLASH] Input files:
[FLASH]     /data/MicrobiomaFrangos/output/fastp/JVMS2_cleaned_R1.fastq
[FLASH]     /data/MicrobiomaFrangos/output/fastp/JVMS2_cleaned_R2.fastq
[FLASH]  
[FLASH] Output files:
[FLASH]     /data/MicrobiomaFrangos/output/flash/pos/JVMS2.extendedFrags.fastq
[FLASH]     /data/MicrobiomaFrangos/output/flash/pos/JVMS2.notCombined_1.fastq
[FLASH]     /data/MicrobiomaFrangos/output/flash/pos/JVMS2.notCombined_2.fastq
[FLASH]     /data/MicrobiomaFrangos/output/flash/pos/JVMS2.hist
[FLASH]     /data/MicrobiomaFrangos/output/flash/pos/JVMS2.histogram
[FLASH]  
[FLASH] Parameters:
[FLASH]     Min overlap:           15
[FLASH]     Max overlap:           250
[FLASH]     Max mismatch density:  0.200000
[FLASH]     Allow "outie" pairs:   false
[FLASH]     Cap mismatch quals:    false
[FLASH]     Combiner threads:      10
[FLASH]     Input format:          FASTQ, phred_offset=33
[FLASH]     Output format:         FASTQ, phred_offset=33
[FLASH]  
[FLASH] Starting reader and writer threads
[FLASH] Starting 10 combiner threads
[FLASH] Processed 25000 read pairs
[FLASH] Processed 50000 read pairs
[FLASH] Processed 75000 read pairs
[FLASH] Processed 100000 read pairs
[FLASH] Processed 116755 read pairs
[FLASH]  
[FLASH] Read combination statistics:
[FLASH]     Total pairs:      116755
[FLASH]     Combined pairs:   114501
[FLASH]     Uncombined pairs: 2254
[FLASH]     Percent combined: 98.07%
[FLASH]  
[FLASH] Writing histogram files.
[FLASH]  
[FLASH] FLASH v1.2.11 complete!
[FLASH] 0.789 seconds elapsed