run fastqc

Question

[Ana]

Hi all- I am new in the bioinformatic and I was running fastqC on my sample using the following:

fastqc *.fastq -o quality

but I have received the following error:

Failed to process 657-07-24-19_R_filt_trim.fastq
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
    at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
    at uk.ac.babraham.FastQC.Sequence.FastQFile.<init>(FastQFile.java:89)
    at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
    at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
    at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:159)
    at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:121)
    at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)

Could you please, help with that? Thanks

Answer 1

[Mensur Dlakic]

It says right there at the top:

Failed to process 657-07-24-19_R_filt_trim.fastq
uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' at

It would appear that your file is not in proper format. It may give us more clues if you type the following and let us know the screen output:

head 657-07-24-19_R_filt_trim.fastq

Cool title - it could be a hip-hop group name.

[Ana]

Thank you for your answer! This is what I get.

?َ??.x??E_os?FR?@????\4???R?l??̴??U???,?<???|YQ]2Q??????????W]??? p????,ޤ?>?????G??t@?'+|??|????jg???9??0?a4??+???Q??Z??2???s ?)???E?%????U????_?ח???Z?/x?o?'4?=??_pX +?1npN_;?m??)????sQ]D&??~???'<?p??×?!????MH?3):????? ?ѵ??????5?rfp}x??j ~A?J? ?X).???R??x(G?.ac]]?b??D?????@??ʄ????G? ?TX?9fj??o[&c -ӼDEz??&DWD??@?Hk ??h??N??G????1H?hk=??.а????n?E-,?3'?VQ?@??j?a? ߉6:\??(D/"-y??/????D??Gk?[?鼴G H?pr$Ɋ ???R??????[ T???A??z? J%-{?x"K??Sk?dUYU??5 ??\J?,!??;5?l??[-?^?wwڴ?j?۶???Fx?t?i??q?????????4??Urɟ?>??@J??$HA?H?>|Hx?;?KD?H x?(???n???ϕ굒Zw?hm8????n o ??8?O!?+|)QTz9?9l?K????,!U???z??t?? ?X?FVR[$Hń???4??u? m????2?7?ȗ ?/??U!{Q??Vٲf类g?f????V???+????N@E??uoz?GA??E????w!}}??????=?wj??R?Ć#ڒ? ?q?[?H??m?.{ ??uo*]5??A? ?D^??Wt?V?Vw\6Zg,??7s?Xq?F)ы~Q|?𺒅???Yʑ?&???7>@????LR?HuɑJ?D^zªzPy@???J?v?Z?5RW}רJ?f?r?k??????f\?*?2K2?T?b<???G?T=?K??ݡ???Zv?}?ZjQ?F^9??????a??\?%?????I CT"?Q?1i??Y]WM????R?tC]7?d}???͛??.?ӍH ?I???&??EQ??R^7T??e?L ?6?邉?S?;?]? a]0[??-oe?Z?????Rt@???+?5gT}b,mtg? M?6~z?????@Y ?8?????Q?][?$^? ?(???'g{?5)???+?? 0Pg??Z?@<??e??)?+???xAka???t??(HS???^vT?㥞?&H????O?~͐~?0???H?h Or%\????+┨,鎗~ ?"/u?CJ?(??ڀpA?BK?R?F?q?%? ??????BW???Λ?@?H??ͥ?????[ %ݕu?7J4FH+???Mg;?Q?SzNK?tg??K<}m?zJ@U??"N5?'?@㔠??y)??? ?pӚ?R?z??Q?eJ?B7???4A?????$? ??~?D?f??,?$

[ATpoint]

This gibberish means it is compressed, probably gzip. Can you show how these files have been generated? If you are very new try to follow guided tutorials or use end-to-end pipelines for your jobs.

[Dunois]

Compressed = <filename>.fastq.gz (most likely). If you really want to, running gunzip <filename>.fastq.gz will decompress it, and the gibberish here should get replaced by slightly more palatable gibberish (a snippet of which you can then share with us).