Demultiplexing sequences

liucong2018 · March 2, 2018, 3:45pm

i had a problem when I demultiplexed sequences.

(qiime2-2017.12) ubuntu@ip-172-31-12-130:~/LC/20180127_LC18SLibrary_3-1_11-1_PE250_RawData$ qiime cutadapt demux-single \

--i-seqs 18S-5-raw-R2.qza
--m-barcodes-file /home/ubuntu/LC/sample-metadata-18S-5.txt
--m-barcodes-category BarcodeSequence
--o-per-sample-sequences 18S-5-raw-demux.qza
--o-untrimmed-sequences 18S-5-raw-untrimmed.qza

Plugin error from cutadapt:
/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-x1uiiltq/M16_GTCCGC_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:
Missing sequence for record beginning on line 5
Debug info has been saved to /tmp/qiime2-q2cli-err-wzu7_gcr.log

Next I did the command:
(qiime2-2017.12) ubuntu@ip-172-31-5-53:~/LC$ gzip -cd s18Swenku5-1_H5MKGBCX2_L1_2.fq.gz | head -n 20
@HISEQ:733:H5MKGBCX2:1:1101:1442:2249 2:N:0:CATCAAGT
AGTCAATGATCCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCTAAGTGATATGGTTTACTTGATTTTCCGCGCTTGCGCGCAGTCCAAAAGGTTCACCGGACCACTCGAAATCGGTAGGAGCGACGGGCGGTGTGTACCGTGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAGAGTCAAGAGGGTCGACCGG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIHHIIIIGIIIIIIHHIGHIIHIIIIIIHHIIHHIIIIIHIIIHIHIIHIEGHHIIIIIIIIIIIIIIIIHIHIHGHEHIIIIHGHIGHH?<HHHHIIIGHHHIIHHHHHHGHIHDHIDHHH?HGHIIAFHHIIIEHIHIHHHHIIHIDEHI7BFHIIIHHEHEH-FEEHFHFEFGFHGHHHIGHH6E?-@-G@@EC->DHGC#####################
@HISEQ:733:H5MKGBCX2:1:1101:1903:2212 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTACTACCGATTGAATGGCTTAGTGAGGTCTTCGGATTGACCTACAGATTCCCGCAAGGGAGCCTGTAGGACGAGAAGTTGATCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATACAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA
+
@DDDAHHIIIIIHHHHIHHHIIIIIIIHHHIIIIHIIHIIGIHHIHIIHHIIIIHGHHIIHHIIIIGHIEHH@GHIIIIHIIIEHIGHHHIFHHHIIIIHIHGIHIIIIEIEHHHFHHHHHHHCHHIEHHHI?EHEHHIHIIIHHIIII?HDHIIHIIIIIIIIGHHIIIIIIGIIIIIC@EHIIHHHHHHEIEHIIICGAGHHIECHHGHFHHEHIGEEHHHHHGEHH<@<,5@GHEGCEHII+>=DH#
@HISEQ:733:H5MKGBCX2:1:1101:2821:2240 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGCGAAATCTTCAGATTGCTGGCGAGGCTAACCCCTCGCTGTGAGAAGTTGATTAAACCTTATCATCTAGAGGAAGGAGAAGCCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATTGACTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAA
+
DDDDCIGIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIHHIIHIIIIIIHIIIIIGHIIGHIIIIIIIGHIIIHHIIIIIIIHHHIIIHHHIIIIIIHGHIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIIIHIIIIIIIIGIIIIIIIIIIIHIIIIIHIIIIIIIIIIIIIIIIIIIEHGHHDHHHHIIIICEHIHIEEHHGHHHHIIIIIIGGCDCH>G?GHHI?EGHHHIDD###########
@HISEQ:733:H5MKGBCX2:1:1101:3025:2233 2:N:0:CATCAAGT
CGATGTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAATTTTCGGACTGAGGTTGAGGGCCGCAAGGTTACTCAACAGCGGGAAGTTACTTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATGGTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAGAC
+
DDDDDIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIHIIIHIIIIIIIHIIIIIIIIIIHIIIIICEHIIIIIIIHIIIIIHHIHHIIIIIIIIGIIIIIIIHIHHHIHIIIIIIIIIIIHHHIIIIGIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIHIIIIIIIIHHGHHIIIGIHI=HHHIH<HHHDHHIHHIHHFHIIHIIIIHIHGHIHECHIHIHCHIIHIHH@GHGHHHHI######
@HISEQ:733:H5MKGBCX2:1:1101:3353:2192 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTCCTACCGATTGGATGTGCTGGTGAAGTGTTCGGATTGGCATCGGTTGGTGGCAACACTGGCCGGAGCCGAGAAGATCATTAAACCCTCCCATCTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATACAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIHIHIIIIIIIIIGIIIIIIIIIIIIHIIIIIHIIIIIIIIIIIIIIIIIIIIHIIIIIIIHIGIHHHIIHHHHIIHHD?HHHIHIIHHHGHHHHIIIHIFHIIHHIHHIHIICHHIHIIHHIIIIDHIH###

I can not find why it had mistakes. who can tell me the reason?help!
Thanks a lot.

thermokarst · March 2, 2018, 6:16pm

Hi @liucong2018!

I think this part of the error message is letting you know that something is wrong with your source data. Do you still have your reads somewhere? You could run the follow:

 gzip -cd /path/to/your/sequences.fastq.gz | head -n 20

Where /path/to/your/sequences.fastq.gz is the file that has your reads in it. Can you run that command and send the results this way?

Thanks!

liucong2018 · March 5, 2018, 2:25pm

ubuntu@ip-172-31-42-26:~/LC$ gzip -cd s18Swenku5-1_H5MKGBCX2_L1_2.fq.gz | head -n 20
@HISEQ:733:H5MKGBCX2:1:1101:1442:2249 2:N:0:CATCAAGT
AGTCAATGATCCTTCTGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCTAAGTGATATGGTTTACTTGATTTTCCGCGCTTGCGCGCAGTCCAAAAGGTTCACCGGACCACTCGAAATCGGTAGGAGCGACGGGCGGTGTGTACCGTGATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAGAGTCAAGAGGGTCGACCGG
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIHHIIIIGIIIIIIHHIGHIIHIIIIIIHHIIHHIIIIIHIIIHIHIIHIEGHHIIIIIIIIIIIIIIIIHIHIHGHEHIIIIHGHIGHH?<HHHHIIIGHHHIIHHHHHHGHIHDHIDHHH?HGHIIAFHHIIIEHIHIHHHHIIHIDEHI7BFHIIIHHEHEH-FEEHFHFEFGFHGHHHIGHH6E?-@-G@@EC->DHGC#####################
@HISEQ:733:H5MKGBCX2:1:1101:1903:2212 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTACTACCGATTGAATGGCTTAGTGAGGTCTTCGGATTGACCTACAGATTCCCGCAAGGGAGCCTGTAGGACGAGAAGTTGATCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATACAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA
+
@DDDAHHIIIIIHHHHIHHHIIIIIIIHHHIIIIHIIHIIGIHHIHIIHHIIIIHGHHIIHHIIIIGHIEHH@GHIIIIHIIIEHIGHHHIFHHHIIIIHIHGIHIIIIEIEHHHFHHHHHHHCHHIEHHHI?EHEHHIHIIIHHIIII?HDHIIHIIIIIIIIGHHIIIIIIGIIIIIC@EHIIHHHHHHEIEHIIICGAGHHIECHHGHFHHEHIGEEHHHHHGEHH<@<,5@GHEGCEHII+>=DH#
@HISEQ:733:H5MKGBCX2:1:1101:2821:2240 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGCGAAATCTTCAGATTGCTGGCGAGGCTAACCCCTCGCTGTGAGAAGTTGATTAAACCTTATCATCTAGAGGAAGGAGAAGCCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATTGACTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAA
+
DDDDCIGIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIHHIIHIIIIIIHIIIIIGHIIGHIIIIIIIGHIIIHHIIIIIIIHHHIIIHHHIIIIIIHGHIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIIIHIIIIIIIIGIIIIIIIIIIIHIIIIIHIIIIIIIIIIIIIIIIIIIEHGHHDHHHHIIIICEHIHIEEHHGHHHHIIIIIIGGCDCH>G?GHHI?EGHHHIDD###########
@HISEQ:733:H5MKGBCX2:1:1101:3025:2233 2:N:0:CATCAAGT
CGATGTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAATTTTCGGACTGAGGTTGAGGGCCGCAAGGTTACTCAACAGCGGGAAGTTACTTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATGGTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAGAC
+
DDDDDIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIHIIIHIIIIIIIHIIIIIIIIIIHIIIIICEHIIIIIIIHIIIIIHHIHHIIIIIIIIGIIIIIIIHIHHHIHIIIIIIIIIIIHHHIIIIGIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIHIIIIIIIIHHGHHIIIGIHI=HHHIH<HHHDHHIHHIHHFHIIHIIIIHIHGHIHECHIHIHCHIIHIHH@GHGHHHHI######
@HISEQ:733:H5MKGBCX2:1:1101:3353:2192 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTCCTACCGATTGGATGTGCTGGTGAAGTGTTCGGATTGGCATCGGTTGGTGGCAACACTGGCCGGAGCCGAGAAGATCATTAAACCCTCCCATCTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATACAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAA
+
DDDDDIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIHIHIIIIIIIIIGIIIIIIIIIIIIHIIIIIHIIIIIIIIIIIIIIIIIIIIHIIIIIIIHIGIHHHIIHHHHIIHHD?HHHIHIIHHHGHHHHIIIHIFHIIHHIHHIHIICHHIHIIHHIIIIDHIH###

thermokarst · March 6, 2018, 12:17am

Hmm, everything looks good here - maybe you could try reimporting and trying again? I wonder if a file was corrupted somewhere in the process. Keep us posted!

liucong2018 · March 6, 2018, 2:51pm

Thanks a lot. I will have a try again.

system · April 6, 2018, 8:51pm

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