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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Minimum header requirements to be accepted as input? #223

Open lightworms opened 5 months ago

lightworms commented 5 months ago

Hello!

I'm trying to assemble the mitogenome for sequence data that has the following header format which seems to have been edited, any idea if I can modify it so that it's accepted as input?

Forwards: @SRR17088602.9 9/1 GNATCCTTGGATAAATTTATCTACTATTGGTTATAAAAAAGTTATGATAGGGAAATTAAAAAATATCGGATATTAATTGACACTTAAGAACTTCAAAGTGATGTGGCATCTCGAATTCAAATCCGTTTTGCTATATTAATAACTCGTTAG + F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFF::F,:F: @SRR17088602.10 10/1 TNATTGTTTCCCCTCCAAGATTAGAAAAGAGAATAAAAAGACATGTTCCTTCTTCACCACCACTACTACCAAAAGAGAGTCAAGTATAAATTATTTTTTTTCAAAAATATTTTAATTACTTTTCTTAGCTATCTTCGCCACCAAGAATAG + F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,FFFFFFF::F::FFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFF

Reverse: @SRR17088602.4 4/2 GTTATGATAGAAAAATTAAAAAATATCGGATATTAATTGACACTTAAGAACTTCACAGTGATGTGGCATCTCGAATTCAAATCCGTTTTGAAATATTAATAGCTCGTTAGAATCAGCATGAAAAACTGTATTAGAATCCTTGGATAAATT + F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFF,FFFFFFFFFFFFFF,FFFFFFFFFF @SRR17088602.5 5/2 GGAATGTTCTAAAGGATCTTTCAGTAACTGAATTTCCTTGAGACCAATGCGGTGTTGCATAGCTTTTGTTAATGTATAGCATTGAACAGAAATCCTTAAAGAACTCGCTTGTGAAAGCTGTGGCATTGTCAGTTACTAGCTCTACGCAGC + FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

All the best.

ndierckx commented 5 months ago

Hi,

The reads you show here, are they each others pair, because the ids are not matching in any way.. And have you tried to run it already?

lightworms commented 5 months ago

Hello again! Yes sorry I copy and pasted random sections from the forwards and reverse files in proper order it would look something like this: Forwards: @SRR17088602.1 1/1 ANAATTCTGGATCTCTAGGGGACACGGTATAAATTCTTCCGATACGAGGTTTACGATTTTTATTTTTCTCAGAAATATTTAACTTTTTCCAAACTTTATCATTTTTATTAAATGCATATGTTTCAGGAATATTTTCAAAAAGAATATTTT + F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @SRR17088602.2 2/1 TNTATATTTACACACCTGGAGGCAGTTTTCTAAAATTTTTGACTAATAAGGAAAATTCGAGAGGACCAAAAAAATTTTTTCTAAAGGACCCAAAAACATCGACAAAAATCCCCCAATTTTCCTAATTAGTCTTTTGATAATATTCGTAAT + F#FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

Reverse: @SRR17088602.1 1/2 TTTCAAATATGCATTTTTATCACATATAGTAATACCGTTAAGTATTCATTTACCAGACAACCAGAAAATTTATTTTACGAGTAAAAATGCAAGTAAAATTATTAGTGCTATTAATGCAGGTAAAATTCCAGATTCACGTCTTTCGGCTTA + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF @SRR17088602.2 2/2 TGTGGAATAAGTTTTGAACAAAAATTGGGATTTTTTAAATTTGACAACGAATTTTTCATACAAAAATTTTTTGGAGGATGTAGAGAGACTACAAAAAAATTTATTCCACAATTTTTAAATAAATTACGAATATTATCAAAAGACTAATTA + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

I Did try to run it and got the following error (Log file is attached) : THE INPUT READS HAVE AN INCORRECT FILE FORMAT! PLEASE SEND ME THE ID STRUCTURE! log_SRR17088602_Arenaria_Test.txt

One way I could make it work though was by changing the format of the file from fastq to fasta.

All the best and thank you for taking the time to respond.