Problems with importing data after some manipulations

Hello Qiimers! :sunglasses:

I have sequences in single reads:

Barpear_NP_11-Endo-AT_S18_L001_R1_001.fastq.gz Barpear_NP_7-Exo-AT_S13_L001_R1_001.fastq.gz Barpear_NP_NTC2_S22_L001_R1_001.fastq.gz Barpear_NP_11-Exo-AT_S17_L001_R1_001.fastq.gz Barpear_NP_9-Endo-AT_S16_L001_R1_001.fastq.gz Barpear_NP_NTC_S19_L001_R1_001.fastq.gz Barpear_NP_1-Endo-AT_S8_L001_R1_001.fastq.gz Barpear_NP_9-Exo-AT_S15_L001_R1_001.fastq.gz Barpear_NP_S10-AT_S5_L001_R1_001.fastq.gz Barpear_NP_1-Exo-AT_S7_L001_R1_001.fastq.gz Barpear_NP_core7_10S-Ashraf_S1_L001_R1_001.fastq.gz Barpear_NP_S12-AT_S6_L001_R1_001.fastq.gz Barpear_NP_3-Endo-AT_S10_L001_R1_001.fastq.gz Barpear_NP_core7_12S-Ashraf_S2_L001_R1_001.fastq.gz Barpear_NP_S2-AT_S1_L001_R1_001.fastq.gz Barpear_NP_3-Exo-AT_S9_L001_R1_001.fastq.gz Barpear_NP_core7_2S-Ashraf_S3_L001_R1_001.fastq.gz Barpear_NP_S4-AT_S2_L001_R1_001.fastq.gz Barpear_NP_5-Endo-AT_S12_L001_R1_001.fastq.gz Barpear_NP_core7_4S-Ashraf_S4_L001_R1_001.fastq.gz Barpear_NP_S6-AT_S3_L001_R1_001.fastq.gz Barpear_NP_5-Exo-AT_S11_L001_R1_001.fastq.gz Barpear_NP_core7_6S-Ashraf_S5_L001_R1_001.fastq.gz Barpear_NP_S8-AT_S4_L001_R1_001.fastq.gz Barpear_NP_7-Endo-AT_S14_L001_R1_001.fastq.gz Barpear_NP_core7_8S-Ashraf_S6_L001_R1_001.fastq.gz

I tried with:

   qiime tools import \
          --type 'SampleData[SequencesWithQuality]' \
          --input-path new \
          --input-format CasavaOneEightSingleLanePerSampleDirFmt \
          --output-path demux-single-end.qza

and i got this error:

There was a problem importing new:

  new/Barpear_NP_3-Endo-AT_S10_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:

  Header on line 13 is not FASTQ, records may be misaligned

NOTE: 1. When i tried to import particular files it worked, i don’t understand why.
2. Those file were paired-end reads and i did some manipulation on the files before i tried to import them (PEAR, Bowtie and some other name changing)

thank you all :smiley::smiley:

Hi @Yos.Dos,

If you were to decompress Barpear_NP_3-Endo-AT_S10_L001_R1_001.fastq.gz (with something like gunzip or whatever utility your OS has baked in), what is in the first 15 lines?

Hey,
Thanks for you response.
This are the first lines of this sample… (head):

@3-Endo-AT_S10.1101.17161.1634 1.N.0.AGCCTATC
GTGTCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTTCCAATCTGGTGTACGGTAGGGGAAGAGGGAAGTTCCGGTGGAGCGGTGAAATGCGGAGAGATAGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATGGGATTAGAAACCCGCGTAGTA
+
1>1AAFFFFFFAGGGCFA0DGGC000C0B1B111//BE/B2D////B11DD10/0/>///DB/BEE/G221F1/0BFGHF/[email protected]/>?>EE//1F<EC11//<FC11<B?G0/001//?//>//<11<>11>111<>111/HIIII<II==>1GCGGDF??/////<@1CCB</BB2FGC?//<B1F2GBB21BHHGFFE?/?0/E>//E/HHGBB1B/0000//>?>//2D2D1AEF2D21FABA/B/FHFDA0/EEEEFEA2ABB11EFB22FGEF>01111B1>>11
@3-Endo-AT_S10.1101.13462.1635 1.N.0.AGCCTATC
GTGTCAGCAGCCGCGGTAAGACGGGGGGGGCTAGTGTTCTTCGGATTTACTGGGCGTAAAGGGCACGTAGGCGGTGTATCGGGTTGTATGTGAAATTCGCCAACTCCTCCCGGAATGCTCTCTTAACCCTTTCACTTTGGTGAGACAGAGGAGAGTGGAATTTCGAGTGTAGGGGTGAAATCCGCAAATCTACGAAGGAAGACCAAAAGCGAAGGCAGCTCACTGGGACCCTACCGACGCTGGGGTGCGAAAGCATGGGGAGCGAACAGGATTAGAAACCCGAGTAGAA
+
1>1>AFFFDFFAEEGGGEA1BF?0A///--9---99BF/BBF----;//9;//---;---//---9-;---/--;--/;/99-;A--///;//////;--9---//99-/;----9//9;9//////.--;BB/BF///II=FH1?IIIIIGHGF1DF??/0//@[email protected]/F>0DF2DGB>/</>1F2B//0F/F2GEFFB1//1G>F>?/[email protected]@111111>?B0////A//EB/0//A/AA/A/EHGDA0A0AAAABA03FF1GBBB33F1EF>11113B1>>11
--

Thanks @Yos.Dos,

Would you be able to run head with something like -n 15? It looks like line 13 is specifically suspect.

And then you can paste in your response with a “code fence” which will avoid treating any of the contents like markup:

```text
The triple backtick (~` key) will treat everything within it as un-formatted text.
Adding "text" or a language like "bash" at the end of the starting fence will set the
syntax highlighting.
```

Thank you :football:

here there are:

@3-Endo-AT_S10.1101.17161.1634 1.N.0.AGCCTATC
GTGTCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTTCCAATCTGGTGTACGGTAGGGGAAGAGGGAAGTTCCGGTGGAGCGGTGAAATGCGGAGAGATAGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATGGGATTAGAAACCCGCGTAGTA
+
1>1AAFFFFFFAGGGCFA0DGGC000C0B1B111//BE/B2D////B11DD10/0/>///DB/BEE/G221F1/0BFGHF/[email protected]/>?>EE//1F<EC11//<FC11<B?G0/001//?//>//<11<>11>111<>111/HIIII<II==>1GCGGDF??/////<@1CCB</BB2FGC?//<B1F2GBB21BHHGFFE?/?0/E>//E/HHGBB1B/0000//>?>//2D2D1AEF2D21FABA/B/FHFDA0/EEEEFEA2ABB11EFB22FGEF>01111B1>>11
@3-Endo-AT_S10.1101.13462.1635 1.N.0.AGCCTATC
GTGTCAGCAGCCGCGGTAAGACGGGGGGGGCTAGTGTTCTTCGGATTTACTGGGCGTAAAGGGCACGTAGGCGGTGTATCGGGTTGTATGTGAAATTCGCCAACTCCTCCCGGAATGCTCTCTTAACCCTTTCACTTTGGTGAGACAGAGGAGAGTGGAATTTCGAGTGTAGGGGTGAAATCCGCAAATCTACGAAGGAAGACCAAAAGCGAAGGCAGCTCACTGGGACCCTACCGACGCTGGGGTGCGAAAGCATGGGGAGCGAACAGGATTAGAAACCCGAGTAGAA
+
1>1>AFFFDFFAEEGGGEA1BF?0A///--9---99BF/BBF----;//9;//---;---//---9-;---/--;--/;/99-;A--///;//////;--9---//99-/;----9//9;9//////.--;BB/BF///II=FH1?IIIIIGHGF1DF??/0//@[email protected]/F>0DF2DGB>/</>1F2B//0F/F2GEFFB1//1G>F>?/[email protected]@111111>?B0////A//EB/0//A/AA/A/EHGDA0A0AAAABA03FF1GBBB33F1EF>11113B1>>11
--
@3-Endo-AT_S10.1101.17575.1666 1.N.0.AGCCTATC
GTGTCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTCCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGCAGAGGGAATTTCCGGGGGAGCGGTGAAATGCGTAGAGATCGGAAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGACACTGACACTGAGAGACGAAAGCTAGGGGAGCGAATGGGATTAGAAACCCCCGTAGTA
+
3A?ABFFFFFFBEGGCEAC35DGC33E2BAC35AA2BE2FFG1010B33DD5B1B0>[email protected]??GFGHH133FEFE?E/EED/BFDFG3B//[email protected]/<[email protected]@DH11<F1><1<0<<1/..IIHGHIIIIGD0HHHGFHG<----?A?/ECA//FF2GFE?/</B2HFGB?//HHHGGFE?/?0/E>/[email protected]/000B//@?>//[email protected]/FHGDA0/HFEEEEA2BFB1FFAB2AGDEE>01111B1>>11
--
@3-Endo-AT_S10.1101.17465.1684 1.N.0.AGCCTATC
1 Like

OK, thank you @ebolyen
i solved my problem.
the two dashes that somehow (i guess with grep), entered my sequences did all the mess.
so i just removed those line away.
thank you again!

1 Like

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