vsearch icon indicating copy to clipboard operation
vsearch copied to clipboard

Why FASTQ quality value above qmax is treated as Fatal error?

Open billzt opened this issue 1 year ago • 6 comments

When I used --fastx_filter to trim FASTQ files (seeming like a very easy task),

$ vsearch --fastx_filter in.fastq --fastq_stripleft 20 --fastq_stripright 20  --fastaout out.fa

I encountered Fatal error as

Fatal error: FASTQ quality value (75) above qmax (41)
By default, quality values range from 0 to 41.
To allow higher quality values, please use the option --fastq_qmax 75

So I added --fastq_qmax 75. However another Fatal error occurred

Fatal error: FASTQ quality value (76) above qmax (75)
By default, quality values range from 0 to 41.
To allow higher quality values, please use the option --fastq_qmax 76

An example is https://www.ncbi.nlm.nih.gov/sra/SRR19317902, where its reads look like

@SRR19317902.1 M05585:4:000000000-BPG86:1:1101:8340:1726_CONS_SUB_SUB_CMP length=313
TTTATCTTCATCTATTGGAGCTCCAGGTCCTGCAGTTGACTTGGCTATTTTTTCACTTCACATAGCTGGTGCATCTTCAATTTTAGGTGCTATTAACTTTATCACTACTATATATAATATGCGTGCCCCTGGAATGACACTTCACAAAATGCCTTTGTTTGTTTGGTCCATTTTAGTAACGGCTTTTTTATTACTACTATCCTTACCAGTATTAGCTGGTGCAATCACTATGCTTTTAACCGATAGAAACTTTGGTACAGCTTTTTTTGCAGCAGAAGCTGGAGGTGATCCAGTACTTTTCCAACATCTATTT
+SRR19317902.1 M05585:4:000000000-BPG86:1:1101:8340:1726_CONS_SUB_SUB_CMP length=313
HGIHIHHIIIIIIIHIIHIIIFHIHI:GHFFGHIIHE.EEHEHHBHHHIHHIII>BHHIEEEGIHIHIIIIIIIHHI;HIIIIIHIIIHHIH;GHCGHIlef\abmllj_hQ`ddgX\h]ghigddkkalkab]lfgkcg`lmllmlhi`bYi]imlljblilg^Yll^cklkki^lkmliifhhjmmmmmlmli^^_hmd]hlmlllmlllgIIIHHFIIGHHDCHHGIIIEGCIEHEIIIIIIIIIIIIHIHEIIIIIIIIIHIHHIIIIIHIIIHIIIIIIIIIHIHEIIHHHB>HHHIIHIIHHHIIIH
@SRR19317902.2 M05585:4:000000000-BPG86:1:1101:19814:1776_CONS_SUB_SUB_CMP length=313
ATTATCATCTAAAACCGGACAACCTGATCCAGCAATGCATTTAGCTATTCTGGCGCTACACGTAGCTGGAGCTTCTTCAATTTTAGGACCGATAAATTTTATAACTACAATTCTAAACATGAGAACTCCTGGTATGACACTACATAAGATGCCACTATTTTCATGGTCAATTTTAGTAACTGCGTTTTTACTTCTATTATCTTTACCAGTTTTAGCGGGAGCAATTACAATGCTGCTCACAGACAGAAATTTTGGAACAGCTTTTTTTGAAGCTCAAACAGGAGGAGACCCAGTTTTGTTTCAACATTTATTT
+SRR19317902.2 M05585:4:000000000-BPG86:1:1101:19814:1776_CONS_SUB_SUB_CMP length=313
:G;HEH.=8E=8E>8.9BHEB8..E...EB.8.GEH..E.8BH.8.;E>G..;.-:?-9G><.C6HH>.;D>.D.C;H...E>H...E.;6-B-6.7.9b]Naha^RGfRPb^j]GhgllDKCQUIe\kmcZlll]EKj_`QDedli[E[KHXN,UQ^ajklQbVPcdeGfQXQMUQc:[@4S`EH^k\OPcg[OUjgEcFagjFXEVRQ?MS-@9HHAH;IIIHHGHAHE.HH?E.EE.E.;.>>H?.H.AH>A>IHIIHEH>HCH;E<8..IHEG8EIIIGGE8E..:IEHG8EIIIIIGHIHE>HHEGEH
@SRR19317902.3 M05585:4:000000000-BPG86:1:1101:10609:1789_CONS_SUB_SUB_CMP length=313
TCTAAGTCATATTACGAGCCACTCTGGCGGTGAAGATGATTTAGCTATTTTCAGTTTACATTTATCTGGAGCGAGCAGTATTTTAGGGGCGATTAACTTTATTACCACTATCTTTAACATGCGTGGGCCTGGTCTGGGCTTCCATCGCTTACCTTTATTTGTGTGGTCTGTTCTGATTACGGCCTTCTTACTTCTTCTCTCTTTACCGGTTTTAGCGGGAGCGATTACGATGCTGTTAACGGATCGTAACTTCAATACCTCGTTCTTTGATCCGGCGGGCGGAGGTGACCCTATTTTGTGCCAGCACCTTTTT
+SRR19317902.3 M05585:4:000000000-BPG86:1:1101:10609:1789_CONS_SUB_SUB_CMP length=313
-BGHECE>;;GH;.GB.B--..8>.E>.----.EH.E....E8>E88;.EG;E>EE.G>HG;8EAACA..;.:BH9-D..7>>7EH:FE<<-B>8.<G.f[kkillh[lRR`NN]g[PgfljmbjijZbQcMQZ;>K`PLLaP\I_jcNOS]<]G7OORRZ[]VROMQbkgia]eik]\IaZhVjcdaQ`jhiY^ciaklibdkRehkXYXL^IEEH9IHIF>E>HIGHH:HIHHFGIH.-HEH<HHGHCHHIH;D6??EIIEBH.IHBH<E9<EGGH<E>GH8H>HHCGCEGB8>B>E.HE8:>EB9EGIHH

Above all, what I wondered is why FASTQ quality value above qmax is treated as Fatal error? I had thought that any quality values larger than 41 would be cut off to 41.

billzt avatar May 21 '23 11:05 billzt