Closed jsabban closed 2 weeks ago
Hi @jsabban,
It seems there might be an exception issue with your FASTQ file. To help find the problem, could you please provide the first 4 lines of your FASTQ file?
Ali
Hi @alihamraoui , here are the first 4 lines of my FASTQ file :
@1a790b27-c54a-44b2-b6bb-0066afaf968e runid=6b2d611263610f8f4f521413ba294547e26a6308 read=42 ch=391 start_time=2024-04-16T16:37:38.785785+02:00 flow_cell_id=FAX94246 protocol_group_id=EMPHY sample_id=EMPHY-MLTPXreq-T16-L20-NBD114-24 barcode=barcode01 barcode_alias=barcode01 parent_read_id=1a790b27-c54a-44b2-b6bb-0066afaf968e basecall_model_version_id=dna_r10.4.1_e8.2_400bps_sup@v4.2.0
CCAATTACGTCGTTGTAGTCCAGCAAATACGTTTGTCACACAAACTTCATATTCTGGGCAACTCGGAGAGCGACTTAATGAAACATTTAAAAGATATAAACTACAATGGAAAATACACTTGCACTCATTGAAAACCCTACTCAAGGGCTTAAAACATTATCCGGAACAATTAGTTGGGAAGCTTTTAAACAAAACTGCTTTAAAGGATTTACAACAACGTACTGCACTCTTTACCAGTTGGTATAAAGTCGAATGTTCTGCCAACTTAAACCAGACCAACGTAGTTTAACGAATCGTTACGGGTATAATCCAAACTATCAGCAAACTGGGTCAAGTTCCATGAACCGATTTAAAGATCGTATTAAAGCCCGATTACGCGAATCTACTCACCAAGCACACCCGCTTTATGCAATGTCTGGTTCAATCCGTGGAACCTTTGGAAGCCGTGGGTATGAAACACGACTTCAACGTCCGCTGACTGGTCCTGTAACACAAATGAGTCAGGAATTTTTAAATCTAGTTTAAGTAAATTTCTAAGGGTATCCCATTTTATTGGTACCCCTAGAAATTTTTATATTTAAACATCATATTGTTTTGCGATATACTGGTAGAAAGCTATAATATAAACGAGCATCGTGGATAATAATGGAACCGTTATTAGACGAGAGCTTTGAAAGAAATGTTGAGGATTTCATATGTCAGGATCTACAGGAGAACGTCCTTTTAGTGACATCGTTACTAGTATTCGTTACTGGGTAATTCACAGTGTTACAATTCCGTCACTCTTTATTGCAGGATGGCTTTTTGTAAGTACTGGTTTAGCTTACGATGTATTTGGAACACCGCGTCCAAACGAATACTTTACGGATA
+
EGSSIHGJEDFGSKIIISSRIHILKLKSJOCEFKJMFHLGHEGFEFGEFS<<;;;;FHQHGJG66200588----/--/(((((7520))78:988899:CDGIENGILSKRKLSHLFBC@CLJFKSKMISNSSDABABJMISSSKSSMIGMJIIHJHIJGA56EJE>=77+***+11*54000/*.34@BJSOIINGSLMHJKKKOGMSLFCCCCGSIGSSISGOHFKINLFGGMMLIHSKSS11111=44445C64444DDNNSIISNIHLKJSSLKMMISHFJSLJMOIOKHCJHEG.--.HMBBA/-)))'''''13:;HSIJKLSNJKRKIKPLEEISSHMKISOSFIKSOKMSSKKHISSKSHOLJE>,,,,,FKOEGIHFHFNLMSOSSLNIJKELQMSISOKOSJSHMSGGEL==>=>FIIKSSSJRQMLIHSKJFSSKJMOSLJKKSOS=<<<<CBFSNGOSGSHJGLILSIGSRSSKKOSSKKMSNJJNSSKEJKHLIOLSHKKSP000000FGLSEKHJJJKRJSIRSKKPSHKSINLQSSSMOJJG<G?)<)))DC@EGIILNPFKSSSSKGSGSILSSENSSKSSGFHGNJSHNGGI:::::>QSFIHKSKSMLKKSHJKIJKSHSLSLHSSHGSJJILGSHKJSJJNSIFABBFFECD<??>1:;>@EGEPOJLKMLSNSFSIJS55655644333AAILKPKKISJHPSSLSSMSNHSMPSMGDGDCDKGF22222<<<<@JMSMHJSSIJMSKSNSJJSSSMHSMSOKRSMKD@@@@@SKPGSNRSSSKSIKGGJSSSSDDCDFJK@?@?@CFGFSLGM<77DDDGHJFENSHGEEJSEBDG@CB@>70.,)'&
Hi @jsabban,
Thank you for reporting this issue.
I noticed that in the newer version of FASTQ, the sample_id
flag is used instead of sampleid
, which seems to be part of the problem.
I’ve addressed this issue in commit ab764669c0b21ba09d8aa0fc65207675d25b4a4c.
A new version (2.7.1) will be available tomorrow!
Thank you, Ali
Whoa, so quick ! Thank you for the fix 😃
Hi !
I have an error when I use a FASTQ file as input, I do not understand why... I use the docker image from singularity. I ran that :
And the output is :
Someone can help me, please ?