# UnboundLocalError: local variable 'idx' referenced before assignment **URL:** \ **Category:** MetaPhlAn\ **Created:** [July 14, 2020, 1:53pm UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715 "2020-07-14T13:53:32Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![AQ7](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aq7/32/905_2.png) [@AQ7](https://forum.biobakery.org/u/AQ7)\ **Post date:** [July 14, 2020, 1:53pm UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/1 "2020-07-14T13:53:32Z")
Hello everyone I am using now metaphlan3, installed from github following the indications here ([https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0)) I have runned this command ` metaphlan ../Database/Late_Medieval6_TCAAGGCATCGG_R1.fastq.gz --input_type fastq --bowtie2db bowtie2db -o Profile.txt` and then I get this error: ``` Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1 Downloading file of size: 0.00 MB 0.01 MB 232.33 % 8.91 MB/sec 0 min -0 sec Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAAyoJpOgcjop41VIHAGWIVLa/mpa_latest?dl=1 Downloading file of size: 0.00 MB 0.01 MB 31507.69 % 13.56 MB/sec 0 min -0 sec Downloading MetaPhlAn database Please note due to the size this might take a few minutes File bowtie2db/file_list.txt already present! Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AADlxibskzbPHPoDl6S-FyKka/mpa_v30_CHOCOPhlAn_201901.tar?dl=1 Downloading file of size: 366.62 MB 366.62 MB 100.00 % 4.24 MB/sec 0 min -0 sec Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AACTzoUYDqZps8u2JqWCNCODa/mpa_v30_CHOCOPhlAn_201901.md5?dl=1 Downloading file of size: 0.00 MB 0.01 MB 12800.00 % 11.29 MB/sec 0 min -0 sec Decompressing bowtie2db/mpa_v30_CHOCOPhlAn_201901.fna.bz2 into bowtie2db/mpa_v30_CHOCOPhlAn_201901.fna Building Bowtie2 indexes Removing uncompress database bowtie2db/mpa_v30_CHOCOPhlAn_201901.fna Download complete Traceback (most recent call last): File "/home/.local/bin/read_fastx.py", line 8, in sys.exit(main()) File "/home/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 155, in main nreads += read_and_write_raw(f, opened=False, min_len=min_len) File "/home/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 119, in read_and_write_raw nreads = read_and_write_raw_int(inf, min_len=min_len) File "/home/.local/lib/python3.6/site-packages/metaphlan/utils/read_fastx.py", line 111, in read_and_write_raw_int nreads = idx - discarded UnboundLocalError: local variable 'idx' referenced before assignment ``` What it is happening is not so clear to me, does anyone have any suggestion about how resolve this issue? thanks a lot ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [July 20, 2020, 8:19am UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/2 "2020-07-20T08:19:08Z")
> [@AQ7](#): > > …/Database/Late\_Medieval6\_TCAAGGCATCGG\_R1.fastq.gz Are you sure the file isn’t corrupted? Can you run ` zcat ../Database/Late_Medieval6_TCAAGGCATCGG_R1.fastq.gz | wc -l`? ---
**Author:** ![AQ7](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aq7/32/905_2.png) [@AQ7](https://forum.biobakery.org/u/AQ7)\ **Post date:** [July 20, 2020, 10:32am UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/3 "2020-07-20T10:32:13Z")
I have tried to do zcat as you suggested and I get the following number as results: 583628 What does it means? ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [July 22, 2020, 7:14am UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/4 "2020-07-22T07:14:33Z")
This returns the total numbers of lines in the fastq file, 145907 reads. If you run directly `read_fastx.py -l 70 ` do you get the same error? Also, how did you retrieved your fastq.gz? Have you by any chances downloaded it using Google Chrome? Sometimes it happens that when you download gzip files, Chrome will automatically un-gzip them. ---
**Author:** ![AQ7](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aq7/32/905_2.png) [@AQ7](https://forum.biobakery.org/u/AQ7)\ **Post date:** [July 22, 2020, 9:51am UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/5 "2020-07-22T09:51:14Z")
Hello, yes I have downloaded them but with firefox not chrome, is it the same? I have tried to download them several time but i always get the same problem. If i run the command you suggest I get this: @M\_NS500468:16:H2MNCBGXX:2:21207:15252:11956\_1:N:0:CTCTGCA CGGTTATTTTGCTTGCGGTTCCCCGTATTCCCGTTTCATTGCCTTCGTGGACACGACCCATTGTTTGCCGTATTTGCAGGCATCGACGCCATTTA + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M\_NS500468:16:H2MNCBGXX:2:21207:23030:16556\_1:N:0:CTCTGCA TTGTCTTCCGCAACCAAAATTAAAAAAATGGCATTAGATCGGATGGCAGAAAAAGATGTAAAGGTATATTGCGAAGACAGGGGTGTCGTAGATAAAGAT + JJJ8JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ=JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M\_NS500468:16:H2MNCBGXX:2:21212:22160:2949\_1:N:0:CTCTGCA ATACAGCTGTAAGCTAGAATCATTTGCCACATTCATAATTCTTGAATAAATGTCAGTGGTCATTGTTTTCAGTGGCTTGGAATCACTAGATGCATTGTAT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M\_NS500468:16:H2MNCBGXX:2:21212:21446:12744\_1:N:0:CTCTGCA TTATTTTCAGAGTCAACTTTAATGATCTTTATTTTACCAAGTAAATCACCTTCAATAGTTCCATTTGAAATCGCACTCTTATATTGACTTGTTGCAAT + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ/JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M\_NS500468:16:H2MNCBGXX:2:21212:2531:14147\_1:N:0:CTCTGCA ACTTATAGTGAATTGATCATATCCACAAGGCTCACAGCGTGTGCCAAGCCCTTTTCCTTGATTTGCATCAAGATATCAGGATCCTGTCTTGCCTGATATGATA + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M\_NS500468:16:H2MNCBGXX:2:21212:22463:14223\_1:N:0:CTCTGCA GCTGTCAGCGATGATGAGATGTCGGGATATGTGGATTTGGGACTGATGCAGAATAATATAATCGATTGGGACACCGGTAAAATTTATAGTTTATTTGA + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ @M\_NS500468:16:H2MNCBGXX:2:21301:1661:8770\_1:N:0:CTCTGCA ATTAGAGTCGGTTTTCTTGGTTTCAGATTGTTCTGATTGACTATCTTTCTTGTCATCTTTGTATTCTGCTAACAAGTTTGCTTTGTTATAACCTTCATAAA + JJJJJJJJJJJJJJJJJJJJ8JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [July 22, 2020, 2:38pm UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/6 "2020-07-22T14:38:54Z")
Seems that is working, was the latest line printed something like `#nreads xxxx`? Could you please check which version of MetaPhlAn are you running with `metaphlan -v`? ---
**Author:** ![AQ7](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aq7/32/905_2.png) [@AQ7](https://forum.biobakery.org/u/AQ7)\ **Post date:** [July 22, 2020, 3:17pm UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/7 "2020-07-22T15:17:48Z")
No the latest line printed is this: ``` @M_NS500468:16:H2MNCBGXX:1:23312:22608:20258_1:N:0:CTCTGCA AGATTCAAGAGCGTTATGGCTACACCAAAGAACAGGTAGAAAAAGAATTGAGCGACTGGTTCGGCAAGAATTAAG + JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ@JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ ``` while the metaphlan version is : Metaphlan 3.0 (20 mar 2020) ---
**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\ **Post date:** [July 22, 2020, 3:32pm UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/8 "2020-07-22T15:32:05Z")
I’m not able to reproduce the same error, could you please share with me the fastq? ---
**Author:** ![AQ7](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aq7/32/905_2.png) [@AQ7](https://forum.biobakery.org/u/AQ7)\ **Post date:** [July 22, 2020, 3:48pm UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/9 "2020-07-22T15:48:59Z")
yes of course, I sent you by mail ---
**Author:** ![huminfo8](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/huminfo8/32/1481_2.png) [@huminfo8](https://forum.biobakery.org/u/huminfo8)\ **Post date:** [May 30, 2022, 5:17am UTC](https://forum.biobakery.org/t/unboundlocalerror-local-variable-idx-referenced-before-assignment/715/11 "2022-05-30T05:17:47Z")
@fbeghini Hello from Japan. Is there any progress about tackling this problem? Actually, I encountered same issue. If there is any update I would like to know it.