dstreett
most of reads did not combined
/home/dell/bioinfo/FLASH2/flash2 -M 300 --min-overlap 10 --max-mismatch-density 0.25 /home/dell/bioinfo/FLASH2/C73.RemoveHost_1.fastp.fastq /home/dell/bioinfo/FLASH2/C73.RemoveHost_2.fastp.fastq
[FLASH] Starting FLASH v2.2.00
[FLASH] Fast Length Adjustment of SHort reads
[FLASH]
[FLASH] Input files:
[FLASH] /home/dell/bioinfo/FLASH2/C73.RemoveHost_1.fastp.fastq
[FLASH] /home/dell/bioinfo/FLASH2/C73.RemoveHost_2.fastp.fastq
[FLASH]
[FLASH] Output files:
[FLASH] ./out.extendedFrags.fastq
[FLASH] ./out.notCombined_1.fastq
[FLASH] ./out.notCombined_2.fastq
[FLASH] ./out.hist
[FLASH] ./out.histogram
[FLASH]
[FLASH] Parameters:
[FLASH] Min overlap: 10
[FLASH] Min overlap outie: 35
[FLASH] Max overlap: 300
[FLASH] Max mismatch density: 0.250000
[FLASH] Allow "outie" pairs: true
[FLASH] Cap mismatch quals: false
[FLASH] Combiner threads: 40
[FLASH] Input format: FASTQ, phred_offset=33
[FLASH] Output format: FASTQ, phred_offset=33
[FLASH]
[FLASH] Starting reader and writer threads
[FLASH] Starting 40 combiner threads
[FLASH] Processed 25000 read pairs
[FLASH] Processed 50000 read pairs
[FLASH] Processed 75000 read pairs
.......................................
[FLASH] Processed 26850000 read pairs
[FLASH] Processed 26864060 read pairs
[FLASH]
[FLASH] Read combination statistics:
[FLASH] Total pairs: 26864060
[FLASH] Discarded pairs: 0
[FLASH] Percent Discarded: 0.00%
[FLASH] Combined pairs: 418616
[FLASH] Innie pairs: 411600 (98.32% of combined)
[FLASH] Outie pairs: 7016 (1.68% of combined)
[FLASH] Uncombined pairs: 26445444
[FLASH] Percent combined: 1.56%
[FLASH]
[FLASH] Writing histogram files.
[FLASH]
[FLASH] FLASH v2.2.00 complete!
[FLASH] 309.186 seconds elapsed
most of paired-end reads did not combined
and here list the head of notcombined_1.fastq and notcombined_2.fastq:
dell@dell-PowerEdge-R720:~/bioinfo/FLASH2$ head /home/dell/bioinfo/FLASH2/out.notCombined_1.fastq
@K00137:533:HMNJYBBXX:7:2208:3376:43251 1:N:0
GGCCCGGACTTCTGGCAAGGTAAAGAGAACCCTTTATTTATCGAGTCCGATAACCTTTGTGCCGCATGGAAGAAATATGCTATTGAAAAAGACAACCTCTCTGTCCGCGTAGGCCGCTGGAACATTCCGGGCGAACCTATTGTCATATTG
+
eeeiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii @K00137:533:HMNJYBBXX:7:1228:12601:20832 1:N:0 GACCGCACGTTTGACCGGATTGGTTTCAATCGTATTGACGATGAAGAGTTCCGCAAGCTTGTGAAAGCCCGTCTGGCATATCCAACGAGCAAGGCTGCTACGGTGGAATATCTGAAAAACCACTTTGACGAGGATGTGGATCTTTCAAGA + eeeiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiieiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiieiiiiiiiiiieeiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiieiiiiii
@K00137:533:HMNJYBBXX:7:1111:11393:46487 1:N:0
GGATGAAGTGTTTGCAGGTATTGAACACCTGCAGCATCGGGCGGCCGTCGGCGTCAAAGTTGAGCCGGTAGTGGAACTGCATCTTTCCCGCAAGGCGGGTGTGGTCGCCAGGCTTCCAGTGCAGGAAGTTGGGGCTCCGCTCCATCATGG
dell@dell-PowerEdge-R720:~/bioinfo/FLASH2$ head /home/dell/bioinfo/FLASH2/out.notCombined_2.fastq
@K00137:533:HMNJYBBXX:7:2208:3376:43251 2:N:0
ACAACCTTATCCGTTTCCGTCAGGTTATACCGGTAGAAACTCTCTACCACCTTTCCGGTGGCGTATGCAAACATCGAGGCTTCATCGTAGTCACCGTATGCGTGCAGTGAATCCACCTGATAGTGTTCCCACATCTCCGCATAAATTTCA
+
eeeiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiieiiiieieiiiiiiiiiiiiiiieiiiiiiiieiiiiiiiiiiiiiiiiiiiieeiiiiiiiiiiiiiiiiiiieiiiiiiiiiieeeV[eee` @K00137:533:HMNJYBBXX:7:1228:12601:20832 2:N:0 CTGTGTCGTCCCTCTTTAGAAAAGCCGGTCTTGCGCAAGTCGTCCTCATAATCCGCTTCAAAGTAAAGTGTGGTGACATCATGAATAGCACACCGATATTTCCACCGAACAGTTTTGCTGTATGGCGCACGCTGATGTCCTGTACGACTT + eeiiiiiiiiiiiiiiiiiiieiieiiiiiiiiiiiieiiiiiiiiiiiiiiiiiiiiiieiiiiiieiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiei[eiiiiiiiiiiiiiiiiiiiiiiiiiii
@K00137:533:HMNJYBBXX:7:1111:11393:46487 2:N:0
CTACCGCATCAAAGAGCTGTACGGCTGCACCGGCCGCCCCAACGAGGGCCTGCGCATTGACCCGGTGGAACAGGCCCGGCGCATCCGGGAGGCGGAGCAGAACGACCCCGTGCTGCGGGGGCGGGTGATCCATGGCGTTGCCGACCCGGC
dell@dell-PowerEdge-R720:~/bioinfo/FLASH2$
i wonder how to fix. thanks so much
