paired reads have different names

[Catherine2017]

When dealing with paired reads that have different names, fastp did not report any errors. But bwa will report errors. Does fastp consider paired read by read1 and read2 file position?

[sfchen]

Will add an option to enable read name consistent comparing

[Catherine2017]

Thanks a lot!!!

[ShixiangWang]

Same error when using bwa after preprocessing with fastp.

  [M::bwa_idx_load_from_disk] read 0 ALT contigs
  [W::bseq_read] the 2nd file has fewer sequences.
  [M::process] read 108 sequences (10897 bp)...
  [W::bseq_read] the 2nd file has fewer sequences.
  [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
  [M::mem_pestat] skip orientation FF as there are not enough pairs
  [M::mem_pestat] skip orientation FR as there are not enough pairs
  [M::mem_pestat] skip orientation RF as there are not enough pairs
  [M::mem_pestat] skip orientation RR as there are not enough pairs
  [mem_sam_pe] paired reads have different names: "SRR8652095.142629002", "SRR8652095.142645002"

  [mem_sam_pe] paired reads have different names: "SRR8652095.142629004", "SRR8652095.142645004"

It indeed has different names. How should I rerun the data with fastp to fix the error? @sfchen

$ gunzip -c SRR8652095_1.fq.gz | paste - - - - | cut -f 1| head
@SRR8652095.142629001 142629001 length=101
@SRR8652095.142629002 142629002 length=101
@SRR8652095.142629003 142629003 length=101
@SRR8652095.142629004 142629004 length=101
@SRR8652095.142629005 142629005 length=101
@SRR8652095.142629006 142629006 length=101
@SRR8652095.142629007 142629007 length=101
@SRR8652095.142629008 142629008 length=101
@SRR8652095.142629011 142629011 length=101
@SRR8652095.142629012 142629012 length=101

gzip: SRR8652095_1.fq.gz: unexpected end of file
$ gunzip -c SRR8652095_2.fq.gz | paste - - - - | cut -f 1| head

gzip: SRR8652095_2.fq.gz: unexpected end of file
@SRR8652095.142645001 142645001 length=101
@SRR8652095.142645002 142645002 length=101
@SRR8652095.142645003 142645003 length=101
@SRR8652095.142645004 142645004 length=101
@SRR8652095.142645007 142645007 length=101
@SRR8652095.142645008 142645008 length=101
@SRR8652095.142645012 142645012 length=101
@SRR8652095.142645013 142645013 length=101
@SRR8652095.142645014 142645014 length=101
@SRR8652095.142645015 142645015 length=101

[YeGuoZJU]

Same error when using bwa after preprocessing with fastp.

  [M::bwa_idx_load_from_disk] read 0 ALT contigs
  [W::bseq_read] the 2nd file has fewer sequences.
  [M::process] read 108 sequences (10897 bp)...
  [W::bseq_read] the 2nd file has fewer sequences.
  [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
  [M::mem_pestat] skip orientation FF as there are not enough pairs
  [M::mem_pestat] skip orientation FR as there are not enough pairs
  [M::mem_pestat] skip orientation RF as there are not enough pairs
  [M::mem_pestat] skip orientation RR as there are not enough pairs
  [mem_sam_pe] paired reads have different names: "SRR8652095.142629002", "SRR8652095.142645002"

  [mem_sam_pe] paired reads have different names: "SRR8652095.142629004", "SRR8652095.142645004"

It indeed has different names. How should I rerun the data with fastp to fix the error? @sfchen

$ gunzip -c SRR8652095_1.fq.gz | paste - - - - | cut -f 1| head
@SRR8652095.142629001 142629001 length=101
@SRR8652095.142629002 142629002 length=101
@SRR8652095.142629003 142629003 length=101
@SRR8652095.142629004 142629004 length=101
@SRR8652095.142629005 142629005 length=101
@SRR8652095.142629006 142629006 length=101
@SRR8652095.142629007 142629007 length=101
@SRR8652095.142629008 142629008 length=101
@SRR8652095.142629011 142629011 length=101
@SRR8652095.142629012 142629012 length=101

gzip: SRR8652095_1.fq.gz: unexpected end of file
$ gunzip -c SRR8652095_2.fq.gz | paste - - - - | cut -f 1| head

gzip: SRR8652095_2.fq.gz: unexpected end of file
@SRR8652095.142645001 142645001 length=101
@SRR8652095.142645002 142645002 length=101
@SRR8652095.142645003 142645003 length=101
@SRR8652095.142645004 142645004 length=101
@SRR8652095.142645007 142645007 length=101
@SRR8652095.142645008 142645008 length=101
@SRR8652095.142645012 142645012 length=101
@SRR8652095.142645013 142645013 length=101
@SRR8652095.142645014 142645014 length=101
@SRR8652095.142645015 142645015 length=101

Hello，have you solve this problem, I also get this error

[YeGuoZJU]

Will add an option to enable read name consistent comparing

Have you add it?

[wuzhaoqi1015]

所以到底什么时候可以解决呢？