Entering edit mode
5.8 years ago
kutanfurkan7
•
0
Hello everyone , Today I tried downloading data from hmpdac via portal_client(data_tool I use with python link=https://github.com/IGS/portal_client ).I downloaded successfully aspera manifest.tv.Below code 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 is working image.
However, I downloaded diffrent aspera_manifest.tsv from hmpdac but this is not work It say no such file or directory.Below code is diffrent_manifest.tsv inside:
file_id md5 size urls sample_id
1419f08f554e0c93f3b62fe90c0db7cf 1aafd7a4515c22d131351a05b9528d3d 15322124 fasp://aspera2.ihmpdcc.org/ibd/genome/microbiome/wgs/analysis/hmmrc/CSM79HJY_genefamilies_relab.biom 1419f08f554e0c93f3b62fe90c0d9dfd
1419f08f554e0c93f3b62fe90c0db842 eefaffea20601799c1eb28708093dc17 596905 fasp://aspera2.ihmpdcc.org/ibd/genome/microbiome/wgs/analysis/hmmrc/CSM79HJY_ecs_relab.biom 1419f08f554e0c93f3b62fe90c0d9dfd
1419f08f554e0c93f3b62fe90c0dccc1 cd0637cf3284946e583b04a2a48f58d3 16474 fasp://aspera2.ihmpdcc.org/ibd/genome/microbiome/wgs/analysis/hmscp/CSM79HJY_taxonomic_profile.biom 1419f08f554e0c93f3b62fe90c0d9dfd
1419f08f554e0c93f3b62fe90c0dc1c7 feee2bb8eaf7932cbbe5de750b770387 83427 fasp://aspera2.ihmpdcc.org/ibd/genome/microbiome/wgs/analysis/hmmrc/CSM79HJY_pathabundance_relab.biom 1419f08f554e0c93f3b62fe90c0d9dfd
This is error image:
Have a any idea ? How Can I solve this problem?Thanks for your comment.
kutanfurkan7 : Can you tell how how this question is different than this one from before: Portal_client no valid url in the manifest file error
Hi genomax , before situation depands on url , It didnt find url via portal_client I solved that but now It is finding url and It generate new problem(file not found)I dont understand maybe file location wrong or server problem. (First code use aspera.hmpp server but other use aspera2.ihmpdac) .In addition I checked my ssh and It opened.(port 22 tcp and 33001 udp)Thank for your comment.
Have you tried to put just one entry in the .tsv file to see if things work before putting in several?
Posting screen shots like ones above does not help since we can't see the command you are actually running. You should edit the original post and paste the exact command you are trying to run.
Please edit your post using : How to add images to a Biostars post
Plus all links broken. Please fix.
do you see? Check please
If you can see your pictures in the preview then it is all good. Yes we can see them now thanks
I thank for your comment