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Can not download reference files for running Pathseq pipeline.

Hi GATKer:

I am trying to download the pre-built reference files for running Pathseq pipeline from GATK Resource Bundle FTP server in /bundle/beta/PathSeq/. But it fails with some permission denies for data transferring. Could you double-check the visiting privilege of files under the path /bundle/beta/PathSeq/.

Thank you in advance

Sen ZHAO

Issue · Github
by Sheila

Issue Number
3110
State
closed
Last Updated
Closed By
chandrans

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @senzhao
    Hi Sen,

    I will ask the developer and get back to you.

    -Sheila

  • markwmarkw 7003AMember, Broadie, Moderator, Dev admin

    Hello @senzhao

    How are you accessing the FTP server? Be sure that you are logging in with username gsapubftp-anonymous as described on the resource bundle page.

  • Hi,
    I have an issue trying to download 'pathseq_microbe.tar.gz', my best guess is that the 'pathseq_host.tar.gz' has files for human.fa, to filter the orginal bam file. Taxonomy is needed for microbe classification....and I need pathseq_microbe.tar.gz to compile a gut/colon bacteria FASTA file to help with classification. Wget will link it to the ftp site and intiate the download, but it will not start the download....

    I ran this:
    wget ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz
    --2018-10-24 14:21:03-- ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz
    => ‘pathseq_microbe.tar.gz.4’
    Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251
    Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected.
    Logging in as gsapubftp-anonymous ... Logged in!
    ==> SYST ... done. ==> PWD ... done.
    ==> TYPE I ... done. ==> CWD (1) /bundle/pathseq ... done.
    ==> SIZE pathseq_microbe.tar.gz ... 101527091967
    ==> PASV ... done. ==> RETR pathseq_microbe.tar.gz ... done.
    Length: 101527091967 (95G) (unauthoritative)

    0% [ ] 0 --.-K/s

    And this:

    wget -r 'ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz'
    --2018-10-24 14:28:04-- ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz
    => ‘ftp.broadinstitute.org/bundle/pathseq/.listing’
    Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251
    Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected.
    Logging in as gsapubftp-anonymous ... Logged in!
    ==> SYST ... done. ==> PWD ... done.
    ==> TYPE I ... done. ==> CWD (1) /bundle/pathseq ... done.
    ==> PASV ... done. ==> LIST ... done.

    [ <=>                                   ] 522         --.-K/s   in 0.007s  
    

    2018-10-24 14:28:06 (74.8 KB/s) - ‘ftp.broadinstitute.org/bundle/pathseq/.listing’ saved [522]

    Removed ‘ftp.broadinstitute.org/bundle/pathseq/.listing’.
    --2018-10-24 14:28:06-- ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz
    => ‘ftp.broadinstitute.org/bundle/pathseq/pathseq_microbe.tar.gz’
    ==> CWD not required.
    ==> PASV ... done. ==> RETR pathseq_microbe.tar.gz ... done.
    Length: 101527091967 (95G)

    0% [ ] 0 --.-K/s

    Is there anything wrong with my though process and code here? I would appreciate the help!

    Best,

    -Ashraf

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    HI @shabaneh1019

    I tried it and was able to download the tar file. Maybe try again and let me know if you are still having this issue.

    wget ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz
    --2018-10-30 17:50:59--  ftp://[email protected]/bundle/pathseq/pathseq_microbe.tar.gz
               => ‘pathseq_microbe.tar.gz’
    Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251
    Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected.
    Logging in as gsapubftp-anonymous ... Logged in!
    ==> SYST ... done.    ==> PWD ... done.
    ==> TYPE I ... done.  ==> CWD (1) /bundle/pathseq ... done.
    ==> SIZE pathseq_microbe.tar.gz ... 101527091967
    ==> PASV ... done.    ==> RETR pathseq_microbe.tar.gz ... done.
    Length: 101527091967 (95G) (unauthoritative)
    
    pathseq_microbe.tar   1%[                    ]   1.10G  13.4MB/s    eta 1h 43m 
    
  • shabaneh1019shabaneh1019 Member
    edited October 2018

    I was able to solve this, thank you @bhanuGandham ! The only issue now is I am getting file outputs when running the pipeline and I am not receiving error messages..I believe I posted this on a different forum if you could help with that it would be great, thank you!

  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @shabaneh1019

    I will look into it. thank you.

    Regards
    Bhanu

  • @bhanuGandham thank you, I meant to say no file outputs, sorry for the confusion.

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