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JBerthelier / PiRATE

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
http://doi.org/10.17882/51795
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No internet connection #33

Closed JDepot closed 4 years ago

JDepot commented 4 years ago

I am unable to have internet connection in the PiRATE-VM I tried many network setting including Bridged Adapter, but nothing changes.

Can someone help me?

Many thanks in advance

JBerthelier commented 4 years ago

Dear JDepot,

Sorry for my late answer, did you fix your internet problem ? This is more a VirtualMachine related problem, than a PiRATE galaxy issue. It is difficult to me to help you, this issue can be cause by several factors according to your system.

Please check VirtualBox manual or help threads.

Best regards,

Jeremy

JDepot commented 4 years ago

Dear Jeremy

Thank you for your answer. I managed to fix my internet problem, but I encounter a problem with PASTEClassifier. The log file seems to be stuck at waiting for x job(s). I tried it with a very large file and I tried it with a small file. I waited for days to no avail.

The fasta file I entered has only two entries

QFA_6 TCGGCCTCAGATTGGTAGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAA GAAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAGAGCCCAAGATTGAAA GCTGGCGTCTTCGACGTCCGCATTGTAATCTCAAGAAGCGTTTTCCGCTTCGGACCATGC CTAAGTCCCTTGGAAAAGGGCATCATAGAGGGTGATAATCCCGTACATGGCATGGAGCGC CCGAAGCTTTGTGATACGTTTTCTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGG GTGGTAAATGCCATCTAAGGCTAAATATTGGGGAGAGACCGATAGCGAACAAGTACAGTG ATGGAAAGATGAAAAGAACTTTGAAAAGAGAGTTAAACAGTACGTGAAATTGCCAAAAGG GAAGGGTAGGAGGTCAGAGATGCGTCTTGGAATTCAGCCTTGCTTTTTGCTTGGTGTTTT TTCCAAGTTTGCAGGCCAACGTCGGTTTTGGGCACTGGAGAAGGGTGGAAGGAACGTGGC ACCCCTCGGGGTGTGTTATAGCCTTCCACTGGATACAGCGACCGAGACCGAGGACAGCAG CGTACTCGCAAGAGCGGGCCCTCGGGCACCTTTACGCTTAGGGCGTTGGCATAATGGCCC TCTACCACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGTATGCGAGTCTTTGGGTG GCAAACCCATAGGCGCAATGAAAGTGAATTCAGGTGGGATCCGCAAGGTGCACCATCGAC CGATCCTCACGTCTTTTAAGTCGTGGATTTGAGTAAGAGCATACCTGTTGGGACCCGAAA GATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGC GGTTCTGACGTGCAAATCGATCGTCAAATTTGGGTATAGGGGCGAAAGACTAATCGAACC ATCTAGTAGCTGGTTCCTGCCGAAGTTTCCCTCAGGATAGCAGAAACTCACATCAGTTTT ATGAGGTAAAGCGAATGATTAGAGGCCTTGGGGAAGTAACTTCCTTAACCTATTCTCAAA CTTTAAATGTGTAAGAAGCCCTTGTTACTTTAGTGAACGAGGGCATGCGAATGAGAGTTT CTAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGAACGTTGGGTTA AGGTGCCAAAGTATACGCTCATCAGATACCAGAAAAGGTGTTATTTAGTCTAGACAGTGG GACGGTGGCCATGGAAGTCGGAAACCGCTAAGGAGTGTGTAACAACTCACCCACCGAATT AAGTAGCCCTGAAAATGGATGGCGCTCAAGCGTATCACCGATACCCAACCGTCAGTGTTT AGCGAAGCGCTGACGAGTAGGCAGGCGTGGGGGTCCGTATGGAAGCCTTGGCAGTGATGC TGGGTGGAACGGCCTCTAGTGCAGATCTTGGTGGCAGTAGCAAATATTCAAGTGAGAACC TTGAAGACTGAAGTGAGGAAAGGTTCCACGATTACAGCAATTGAACGTGGGTTAGCCGAT CCTAAGAGATAGGGAAATTCCGTATTAAAGTTGTGCGCTTGTTCGCATCGACCTATCGAA AGGGAAACAGGTTAAAATTCCTGTGCCGGGATGTGGATTTTTGGCGGCAACGCAAACAAA CTAGGAGACGTCGGCGGAAGCCCTGGGGAGAGTTCTTTTCTTTTCTTAACGACACGACCC ACCTCGGAATCAATTTACTTGGAGAAGGGGTAGGTCTGTCGGCAGAGCTAGGTACTTATG CCTGGTCCGGAGCGCTTTCGACGACCCTTGAAAATCCTAGGGAGCGAATAATTTTCACAC CCGGTCGTACTCATAACCGCATCAGGTCCTCAAGGTGAACAGCCTCTAGTTGATAGAATA ATGTAGATAAGGGAAGTCGGCAAATTAGATCCGTAACTTCGGGATAAGGATTGGCTCTAA GGGTTAGGTGGTTCGGGCCTTTGTTGGAAGCGACTGCTGGACCTGTCTGGACTGCTTTGG GCAACTGAGGCGGACCGGACGGGACCGGCGGACGTGGAAGGCATGGGCAGCCTCGCGGCG TCCTTTCCACAATTAATAACCAACTTAGAACTGGTACGGACAAGGGGAATCTGACTGTCT AATTAAAACATAGCATTGCGATGGCCAGAAAGTGGTGTTGACGCAATGTGATTTCTGCCC AGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAAC TATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGA TTAACGAGATTCCCACTGTCCCTATCTACTATCTAGCGAAACCACAGCCAAGGGAACGGG CTTGGCAAAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTTTGACATTGTG AAGAGACATGGAGGGTGTAGAATAAGTGGGAGCTTCTGCGCCGGTGAAATACCACTACCT CCATCGTCTCTTTACTTATCCAATGAAGCGGAGCTGGGTTTAACGACCCACCTTTTGGAC TTAAAAGCATTCATGCTTGATCCGAATTGGAGACATTGTCAGGTGGGGAGTTTGGCTGGG GCGGCACATCTGTTAAACGATAACGCAGGTGTCCTAAGGGGGACTCATGGAGAACAGAAA TCTCCAGTAGAACAAAAGGGTAAAAGTCCCCTTGATTTTGATTTTCAGTGTGAATACAAA CCATGAAAGTGTGGCCTATCGATCCTTTAGATCCTCGGCATTTGAGGCTAGAGGTGCCAG AAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTT TTGATCCTTCGATGTCGGCTCTTCCTATCATACCGAAGCAGAATTCGGTAAGCGTTGGAT TGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTT TACCCTACTGATGGAGGGTTATCGTAACAGTAATTCAACTTAGTACGAGAGGAACTGTTG ATTCGTGTAATTGGTCTTGGCCGTTGTCCAACAGGGCAGTGCGGCGAAGCTACCACACGC TAGATAATGGCTGAACGCCTCTAAGCCAGAATCTGTGCTGGAAGCGATGATGTTGGTCCC GCTTGTATGAAATGCGTAAAAATAAGGCATCTTCGGATGCTTGTGTACCATAGCTGGCGA GGGACGGGCTGTTGGACGGAAAGGTCTGCGGTCTACCTCGTGAATTGCAATCACAATATG AGCGGGGAAAAATCTCTTGCAGACGACTTGAATGGGAAGGGGGTGCTGTAAGCAGTAGAG TGGCCTTGTTGCTACGATCTGCTGAGGCTCAGCCCTATCTTCCACGATTTGTTT QFA_8 TACCTGGTTGATTCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCT AAGTATACGCAAATTATACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTAT TTGATGTTTCTTGCTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCGTAAAAA GCCCCGACTTCTGGAAGGGGTGTATTTATTAGATAAAAACCATCCTCCTCGGAGTTTGGT GATTCATAATAACTTCTCGAATCGCACGGCCTTGTGCTGGCGATGCTTCATTCAAATATC TGCCCTATCAACTGTCGATGGTAGGATAGAGGCCTACCATGGTTGCAACGGGTAACGGGG AATAAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCA GCAGGCGCGCAAATTACCCAATCCCGACACGGGGAGGTAGTGACAATAAATAACAATGCA GGGCCCTTTTGGGTCTTGTAATTGGAATGAGTACAATTTAAATCCCTTAACGAGGAACGA TTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAA AGTTGTTGCAGTTAAAAAGCTCGTAGTTGAAGTTTGGTCTCGGACGCTGGGTCTGCTTAA TTGCATGTACTTGACGGTCCGAGACTTCCTTCTTGGTGAACGGCCGCCTTCGGGTGGTCC GGAACCAGGACTATTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCATAGGCCCGAAT ATATTAGCATGGAATAACAGAATAGGACGTGCGGTTCTATTTTGTTGGTTTCTAGAACTG CCGTAATGATTAAAAGGGACAGCCGGGGGCATTAGTATTTGCACGCTAGAGGTGAAATTC TTGGATTGTGCAAAGACTTCCTACTGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCA AGAACGAAGGTTAGGGTATCGAAAACGATTAGATACCGTTGTAGTCTTAACAGTAAACTA TGCCGACTCCGAATCGGTCGATGCTCATTTCACTGGCTCGATCGGCGCGGTACGAGAAAT CAAAGTTTTTGGGTTCTGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGAAATTGACG GAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCAC CGGGTCCGGACATAGTAAGGATTGACAGATTGATGGCGCTTTCATGATTCTATGGGTGGT GGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGATAACGAACGA GACCTTGACCTGCTAAATAGACGGGTTGACATTTTGTTGGCCCCTTATGTCTTCTTAGAG GGACAATCGACCGTCTAGGTGATGGAGGCAAAAGGCAATAACAGGTCTGTGATGCCCTTA GATGTTCCGGGCTGCACGCGCGCTACACTGACAGAGACAACGAGTGGGGCCCCTTGTCCG AAATGACTGGGTAAACTTGTGAAACTTTGTCGTGCTGGGGATGGAGCTTTGTAATTTTTG CTCTTCAACGAGGAATTCCTAGTAAGCGCAAGTCATCAGCTTGCGTTGACTACGTCCCTG CCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGGCTTAGTGAGGACTTGGGAG AGTACATCGGGGAGCCAGCAATGGCACCCTGACGGCTCAAACTCTTACAAACTTGGTCAT TTAGAGGAAGTAAAAGTCGTAACAAGGTATCTGTAGGTGAACCTGCAGATGGATCATT

JBerthelier commented 4 years ago

Dear JDepot,

If the fasta file that you are showing me is the same than the one you are using: the ">" at the beging of the headers of the both sequences are missing.

If not, can you run again PASTEC with those both sequences, and send me

, this will help me to identificate the error cause.

Best regards,

Jeremy

JDepot commented 4 years ago

Dear Jeremy

Thank you for your reply. Indeed I forgot to paste the ">", but they were in my original file. When I run PASTEC I do not get an error message, but the program runs for days (even though there are only two sequences). The log file looks like this: 2020-04-09 11:30:40 - PASTEClassifier - INFO - START PASTEClassifier parallelized 2020-04-09 11:30:40 - PASTEClassifier - INFO - Fasta file name: genome.fa 2020-04-09 11:30:40 - PASTEClassifier - INFO - Running STEP 1 of PASTEClassifier parallelized: DetectTEFeatures START DetectTEFeatures_parallelized Fasta file name: genome.fa split the sequences in batches Homogeneous in size 20kbp launch the programs on each batch prepare bank 'PiRATE_nucl.fa'... prepare bank 'PiRATE_prot.fa'... prepare bank 'Pfam27.0_GypsyDB_PiRATE_hmmer.hmm'... submitting job(s) with groupid 'genome_detectTEFeaturesParallelized' (2020-04-09 11:32:11) waiting for 1 job(s) with groupid 'genome_detectTEFeaturesParallelized' (2020-04-09 11:32:11)

Thanks in advance

JBerthelier commented 4 years ago

Indeed, with two sequences PASTEC should not take lot of time.

How much ram and core did you configure in the VM ?

Moreover, can you try to launch PASTEC again. Look the log file, and when the message "waiting for 1 job(s) with groupid 'genome_detectTEFeaturesParallelized' " appear, open a new konsol and use "qstat" , you should see the pastec job running

PASTEC use a SGE job scheluder

The state of the job, should be "r" (running).

This article show you an example (part 2 basic) http://oliverelliott.org/article/computing/wik_sge/

Does your PASTEC job is running ?

Best regards

Jeremy