flag for not checking read ids in PE mode?

[avilella]

Hi,

I am testing Paladin as an alternative to Diamond for 2 main reasons:

• pair-end mode
• ability to produce bam files

I can successfully produce bam files in single-end mode, but when feeding it data from the NCBI SRA, the read ids don't seem to be paired, and I get this error below.

Is there a way to tell Paladin to take the R1 + R2 reads as they come without checking if the read ids match between the two?

│ [M::writeReadsProtein] Detecting open reading frames...                                                                                                                                                                                                            │
│ [M::writeReadsProtein] Detected and translated 79304452 open reading frames in 112455309 sequences                                                                                                                                                                 │
│ [M::process] Read 3419102 protein sequences (200000116 AA)...                                                                                                                                                                                                      │
│ [M::process] Read 3408448 protein sequences (200000094 AA)...                                                                                                                                                                                                      │
│ [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: "0:1:1:SRR7107847.1", "SRR7107847.2"                                             0                                                                                                                                 │
│                                                                                                                                                                                                                                                                    │
│ [mem_sam_pe] paired reads have different names: "1:2:2:SRR7107847.2", "SRR7107847.9"                                                                                                                                                                               │
│                                                                                                                                                                                                                                                                    │
│ [mem_sam_pe] paired reads have different names: "0:2:2:SRR7107847.1", "SRR7107847.3"                                                                                                                                                                               │
│                                                                                                                                                                                                                                                                    │
│ [W::sam_read1] Parse error at line 20                                                                                                                                                                                                                              │
│ [main_samview] truncated file.                                                                                                                                                                                                                                     │

[0russ4]

Have you solved it? I've encountered a similar issue as well.