Question: Portal_client no valid url in the manifest file error
0
gravatar for kutanfurkan7
9 days ago by
kutanfurkan70 wrote:

Hello everyone , I dowloaded portal_client to collect data from hmpdac.This client works at normal example_manifest , s3_manifest or ftp manifest but It doesnt wok at aspera_manifest.tsv .It say no valid url in aspera_manifest.csv.I check in aspera_manifest.csv and this is correct.How can I solve this problem? Have a idea? thanks for your comments.

This portal_client link=https://github.com/IGS/portal_client
I use first method my pc is win7.

This inside aspera_manifest.tsv

id  md5 size    urls
07c6c17c2b6f11e98849ef9e212bebbd    ed8e04692fc34da01ee9c430612f6b58    3363519 fasp://aspera.hmpdacc.org/ptb/genome/microbiome/16s/hm16str/EP843963_K10_MCKD.trimmedseqset.fasta.gz

[This system error]

This system error

hmpdacc tool • 143 views
ADD COMMENTlink modified 19 hours ago • written 9 days ago by kutanfurkan70

There is a previous question that is likely related : Hmpdac I can't dowload data at fasp server

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax62k

Are all values in your .tsv file tab-separated?

ADD REPLYlink written 7 days ago by genomax62k

Oh sorry , I close previous question and I am thinking like you.All of them seperated with tab.Below file example_manifest.tsv this is work but aspera manifest.tsv doesnt work. I am thinking maybe fasp server problem. I need IBDMDB data but all of them in fasp server and generally people use linux or mac for enter fasp server.(my system windows)

   id   md5 size    urls
8d65351c0cb6f7eb9726a1c463f1c34e    626b3b87b8958e1db84489d727d16607    2353731 http://downloads.hmpdacc.org/data/HM16STR/HMDEMO/SRP002429/stool/not_affected/SRS066784.fsa,ftp://public-ftp.hmpdacc.org/HM16STR/HMDEMO/SRP002429/stool/not_affected/SRS066784.fsa,s3://human-microbiome-project/HHS/HM16STR/HMDEMO/SRP002429/stool/not_affected/SRS066784.fsa
24a6e7b42b6411e9b215a7d3def1d1a3    b4379188b99818d6e0d82b50ae5482bc    8390803 http://downloads.hmpdacc.org/data/HMR16S/HMDEMO/SRP002429/SRR043474.sff.bz2,ftp://public-ftp.hmpdacc.org/HMR16S/HMDEMO/SRP002429/SRR043474.sff.bz2,s3://human-microbiome-project/DEMO/HMR16S/SRP002429/stool/not_affected/SRS174000.tar.bz2
ADD REPLYlink modified 7 days ago • written 7 days ago by kutanfurkan70

The problem is still going on.

ADD REPLYlink written 1 day ago by kutanfurkan70

Does this data require some kind of authorization for download? Is there support at the data site you can email to ask?

ADD REPLYlink written 21 hours ago by genomax62k

Hello genomax thank for your comments.I can dowload below link via aspera connect.(I entered below link at chrome).Aspera connect ask user id and password and I enter my hmpdacc account .

fasp://aspera.hmpdacc.org/ptb/genome/microbiome/16s/hm16str/EP843963_K10_MCKD.trimmedseqset.fasta.gz

I get this link above manifest_tsv but this link is example link. I have to dowload below link

fasp://aspera2.ihmpdcc.org/ibd/transcriptome/microbiome/raw/CSM5MCXD.tar

This time aspera connect say previous problem It say Error fasp managament terminated unexpectedly.

Between file is that I dowload example_manifest.tsv

ADD REPLYlink modified 19 hours ago • written 19 hours ago by kutanfurkan70

In addition @genomax You are right.My 33001 and 22 ports closed now.I am not reaching my modem admin panel now but today I return my home and I will try opening this port.Aspera use this ports for dowload or uplooad I think

ADD REPLYlink written 19 hours ago by kutanfurkan70

but today I return my home and I will try opening this port

That will probably work. Be careful trying to download data from home. These files will likely be large.

If you want to add images to your post use these instructions: How to add images to a Biostars post

ADD REPLYlink written 19 hours ago by genomax62k

Thanks genomax sorry for my wrongs.

ADD REPLYlink written 19 hours ago by kutanfurkan70

There are no wrongs. You may want to use imgbb image hosting provider as shown in instructions above in future. I can't see the image you posted above perhaps others can.

ADD REPLYlink written 18 hours ago by genomax62k
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