# Problem importing fastq.gz files

**URL:** https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690
**Category:** User Support
**Tags:** fastq, import
**Created:** [November 1, 2017, 3:26pm UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690 "2017-11-01T15:26:08Z")
**Posts on this page:** 6
**Page:** 1

<div class="post-metadata">

### Author: ![Jewelna\_Osei-Poku](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/j/bb73d2/32.png) [@Jewelna\_Osei-Poku](https://forum.qiime2.org/u/Jewelna_Osei-Poku)
#### Post date: [November 1, 2017, 3:26pm UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690/1 "2017-11-01T15:26:08Z")

</div>

Hi,  
I have paired end fastq files that I have converted to fastq.gz using the command below:

```bash
gzip extracted/metagseqs_fastq/*.fastq

```

However, when I try importing the files using

```bash
qiime tools import --type "SampleData[PairedEndSequencesWithQuality]" --input-path fastq_folder --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza

```

I get error as below:

```bash
/Users/Jewelna/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/skbio/io/registry.py:922: FormatIdentificationWarning: '_fastq_sniffer' has encountered a problem.
Please send the following to our issue tracker at
https://github.com/biocore/scikit-bio/issues

Traceback (most recent call last):
  File "/Users/Jewelna/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/skbio/io/registry.py", line 914, in wrapped_sniffer
    return sniffer(fh)
  File "/Users/Jewelna/miniconda3/envs/qiime2-2017.9/lib/python3.5/site-packages/skbio/io/format/fastq.py", line 320, in _fastq_sniffer
    if split_length == 10 and description[1] in 'YN':
IndexError: list index out of range

  FormatIdentificationWarning)
There was a problem importing extracted/metagseqs_fastq:

  extracted/metagseqs_fastq/G1_S35_L001_R2_001.fastq.gz is not a(n)
  FastqGzFormat file

```

Could someone help explain what is happening?

---

<div class="post-metadata">

### Author: ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)
#### Post date: [November 1, 2017, 10:35pm UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690/3 "2017-11-01T22:35:00Z")

</div>

Hi @Jewelna_Osei-Poku! Sounds like scikit-bio, which is being used behind the scenes to handle processing your fastq files is upset! It looks like the `description` portion of the fastq records aren't formatted in a way that scikit-bio is expecting to see. Do you think you could provide at least the first few records of `G1_S35_L001_R2_001.fastq.gz`? That would really help us lock-down the issue. Thanks!

---

<div class="post-metadata">

### Author: ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [November 2, 2017, 10:21pm UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690/5 "2017-11-02T22:21:18Z")

</div>

To add on to @thermokarst's answer. We did end up swapping out some of this code in 2017.10. Since you are using 2017.9, I would recommend upgrading. That should also fix the issue.

---

<div class="post-metadata">

### Author: ![Jewelna\_Osei-Poku](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/j/bb73d2/32.png) [@Jewelna\_Osei-Poku](https://forum.qiime2.org/u/Jewelna_Osei-Poku)
#### Post date: [November 3, 2017, 8:28pm UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690/6 "2017-11-03T20:28:20Z")

</div>

Thank you @thermokarst for the response. Kindly find below to the records requested for the file in question. However, I should say that the error pops up with other files names when I re-run the command, so it is not always the same file that gives the error.

@M01232:58:000000000-B8WPP:1:1101:9955:2217 2:N:0:35  
GCTGCTGGCACGAAGTTAGCCGGTGCTTATTCTTTGGGTACCGTCAGAACAATCGGGTATTAGCCGACTGCTTTTCTTTCCCAACAAAAGGGCTTTACAACCCGAAGGCCTTCTTCACCCACGCGGTATGGCTGGATCAGGCTTGCGCCCATTGTCCACTATTCCCCACTGCTGCCCCCCGTAGGAGACTGGACCGTGTTTCCGTTCCAGATTGGCTGAGCATCCTCTCAGACCAACTACGCATCGTCCCCTTGGGGGTCCTCTACACACACACATAGATAAAACGACATCGGCC  
+  
GGGDEGGCFFFEGGEFEEFFCFDFECFGFGGFGGCGGGGCFEFFGEDGCCAFGFGG\>ECFFD\<\<EFEFG+CFGGFEGGFC,5C=F,C49EFC+BFGFDE?A=FGFC@EDGEEFEF\<EEFFFGGGGGGGGGG,@FEG=:B:D8FGE?+\<B:7DE,@DC3,3:E,E;:\>:E786D,\>,,4=4:C=E8EE,=+\>7E\*= **22** 4:**_3+\*++37/0)94)//97_)8\>)9)._1)1)_:7DF44)17))):_09C_7_517:77)/_\*\*\*_)))()_)8.  
 @M01232:58:000000000-B8WPP:1:1101:17718:2864 2:N:0:35  
GCGGCTGCTGGTAATCGGGAACCTGCACGGGGCCTTGCACCTGGACGGGGTACACGCCACACCGCTGCTGCTGCGAATCGGGAACCTGCACGGGGCCTTGCACCTGGACGGGGTACGCACCACTCCGCTGCTGCTGCGTCACGGCCCGCTGCGCGGGCCCCTGCCCCCTGACGGGGTCCGCACCACCCCGCTGCGGGTGCGACACCGCCCGGTGCCGCAGACGCATCCCGCTACCGTGGTCGCCCGACTGCCGCTCCGGGTCTGGCAGCTTCAGGAGGCGGTGGCGCAGGCGCA  
+  
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGG7FGGGFGGGGDGGGGGGGGGG7FFGCD:\>DFGGGEE++=\>CFFFF\<\<DFFCF[F@FGCCB](mailto:F@FGCCB)+8DFGG\>BF@FCG:FF6\>1\>\*\*\*\*4\<CF **1_211/** 2**\*\*\*A;:8/22\*\*/2::E/8811_5_7)77:)97)_)18_119))0)0/))0)/7)17)8.100))1)))1)00)9./)0)01)944)\*\*+1)_:4)73))9)).))-))))).  
@M01232:58:000000000-B8WPP:1:1101:18878:3414 2:N:0:35  
GCGGCTGCTGGCACGTAGTTGGCCGGAGCTTCTTCTGCAGGTACCGTCATTATCGTCCCTGCTTGAACGAGGTTTACAATCCGAAGACCGTCATCCCTCACGCGGCGTTGCTGCGTCACGCTTTCGCCCATTGCGCAAGATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAGCGTGGCTGATCGTCCTCTCAGACCAGCTACCCGTCGTTGCCTTGGTGAGCCCTTACCCCCCCAACAAGCTGATAGGCCGCGAGCCCCCCCCGAAGCCGAACCCCTT  
+  
BEFCGG@FGF-FFFFCFGGG\<CFGG7+@@EFGGGGGGFGGGFGGGGGGG8\<EEFC@CAAFGF,?,?CFG:?F@:FFFGEFDGFGGF::B:+\>=A\<,:3\>=+8@CEC9++@CF,\>\<CFGGC_3@AFGCF7FG:DF,98,D8EC,:E5CFBF?C,,,A=BCFGGGFGEC9\>90__2=8;/+A_\*/9CF99:?FFGGGG**9\>7)_.1\<09:92_97C4_2)9C627)\>3)03_84\>96=:_;)7_7CC:7(/94).8)7)))4)72\>))1).)  
 @M01232:58:000000000-B8WPP:1:1101:22497:4170 2:N:0:35  
GCGGCTGCTGGCACGTAGTTGGCCGGGGCTTCTTCTGCAGGTACCGTCATCTTCGTCCCTGCTGAAAGGGGGTTACAACCCGAGAGCCTTCATCCCCCACGCGGTGTTGCTGCCTCAGGCTTGCGCCCATTGGGCAAGATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCGGTCCCAGTGTGGCTGACCATCCTCTCAGACCAGCTACCGATCGTCGCCTTTGTCCGCCCTTACCCCACCAAATAGCTAATCGGACGCAGGCCCCTCACACAGCCACATGACCGC  
+  
CDGGGGGDFGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGFFFGGGGGGEGGGGGGGGGGGGF@FDFGFGGGGGGGGGGGGGGGGGGGGGGGGEEGFFFFGGGGG:FFCFFDGGGGGGGCG,@FFG\>FGGGGCCFECFGFGGGGGGGGFCFC,2:DE8EC@CEGGGCCFGCF,:CEGGFE+\>C8:\*/\>\<0++45=ECC;668+8C\>7C7\>07EGGGGG4C)\>CCC\>5**:7\*\*).9))07\>0/17\>54C)_2/:768_2._77C)))1.49C(5))/**)04)).0**2)))  
 @M01232:58:000000000-B8WPP:1:1101:19938:4272 2:N:0:35  
GCGGCTGCTGGCACGTAGTTAGCCGGTGCTTCTTTACCCATTACCGTCACTCACGCTTCGTCACAGGCGAAAGCGGTTTCCAACCCGCAGGCCGTCATCCCCCACGCGGCGTTGCTGCATCTGGCTTCCGCCCATTGTGCACTATTCCCCACTGCTGCCTCCCGTAGTAGTCTGGGCCGTATCCCAGTCCCAATGTGGCCGGTCACCCTCTCCGGCCGGCTACCCGTCACAGCCATTGTAAGCCCCTACCCCACCAACAAGCTGCTCCGCCGCGCTTACACCCCCAACCCCCCA  
+  
FGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGA9\<E8@FFGGGGGGGGFCEFEE,6C@CF\<FG,@DGGDE:\<@@:@C,CCF=CC7+4@+6+48@F[5EE+44@F](mailto:5EE+44@F)FEF:@3CC9\>\<\>3D,@9,\>CFG_\>CGC,,@F9,72727@F2?C7B,,46,\<:C88BE8_1_,6+\>+A_8_A\*\*\*=@+\>+0?C69CF_513_:7)_//2?4:_:_7_/)))799971\<_9\>5\*\*19/0;0967@\<FG47).1.5B@5\>F692_)1\*:\>\>))())//\*\*0)(.),)11C35  
@M01232:58:000000000-B8WPP:1:1101:15116:4846 2:N:0:35  
CGGCTGCTGGCACGTAGTTAGCCGTGGCTTTCTGGTTAGATACCGTCAAGGGATGAACAGTTACTCTCATCCTTGTTCTTCTCTAACAACAGAGTTTTACGATCCGAAAACCTTCTTCACTCACGCGGCGTTGCTCGGTCAGACTTTCGTCCATTGCCGAAGATTCCCTACTGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTTCCAGTGTGGCTGACCATCCTCTCAGACCAGCTAACGAACGTCGCCTTGGGCCGCCATTACCCCTCCCACCAGCTAATCGAACGCA

---

<div class="post-metadata">

### Author: ![Jewelna\_Osei-Poku](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/j/bb73d2/32.png) [@Jewelna\_Osei-Poku](https://forum.qiime2.org/u/Jewelna_Osei-Poku)
#### Post date: [November 3, 2017, 8:28pm UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690/7 "2017-11-03T20:28:22Z")

</div>

Actually, Evan Bolyen was right. Upgrading to 2017.10 solved the issue. Thanks guys.

---

<div class="post-metadata">

### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [December 5, 2017, 2:28am UTC](https://forum.qiime2.org/t/problem-importing-fastq-gz-files/1690/8 "2017-12-05T02:28:39Z")

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