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) [email protected]:~/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?HGHI[email protected][email protected]@EC->DHGC##################### @HISEQ:733:H5MKGBCX2:1:1101:1903:2212 2:N:0:CATCAAGT
ATCACGGTACACACCGCCCGTCGCTACTACCGATTGAATGGCTTAGTGAGGTCTTCGGATTGACCTACAGATTCCCGCAAGGGAGCCTGTAGGACGAGAAGTTGATCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCAGAAGGATCATACAAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAA
+
@DDDAHHII[email protected]GHIIIIHIIIEHIGHHHIFHHHIIIIHIHGIHIIIIEIEHHHFH[email protected]EHIIHHHHHHEIEHIIICGAGHHIECHHGHFHHEHIGEEHHHHHGEHH<@<,[email protected]+>=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<[email protected]###### @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.
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?
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!
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#8
