SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
Import raw PacBio data from *.bax.h5 files reubennowell Pacific Biosciences 4 10-12-2015 09:02 AM
Galaxy to Cummerbund Data Import Issue mclo41 Bioinformatics 5 03-02-2015 10:23 AM
Using t1.micro instance can't import data into smrtPORTAL Fad2012 Pacific Biosciences 12 01-16-2015 12:11 PM
amplicon-import data into the 454 software litali Bioinformatics 0 08-24-2010 10:57 PM

Reply
 
Thread Tools
Old 01-29-2018, 08:19 PM   #1
letunglam
Junior Member
 
Location: Viet nam

Join Date: Jan 2018
Posts: 3
Default Import raw data to SMRTLink

I find raw data (bam file, subread.xml..) from Pacbio. I added to SMRTLink. but when I use this data to assembly by HAGP4, SMRTLink noticed fail.
Can I help me how to add raw data to SMRTLink?
P/s: We have a Pacbio SQUEL.

This is log file when i add subread file to SMRTLink.
Quote:
[INFO] [2018-01-29T21:37:05.659-05:00] Running job-type import_dataset [email protected] in /opt/pacbio/smrtlink/userdata/jobs_root/000/000037
[INFO] [2018-01-29T21:37:06.440-05:00] Can't process this dataset
[INFO] [2018-01-29T21:37:06.485-05:00] Completed running job import_dataset Result -> Success(Right(PacBioDataStore(2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,0.2.1,List(DataStoreFile(36c19ac0-c34b-fc6b-86f2-743a3da771e3,pbscala::import_dataset,PacBio.DataSet.SubreadSet,2410,2018-01-29T21:37:05.659-05:00,2018-01-29T21:37:05.659-05:00,/home/data/pacbio/raw_data/Arabidopsis_data_demo/3_C01_customer/m54113_160914_092411.subreadset.xml,false,pacbio_dataset_subreadset-160923_085639252,Imported DataSet on 2018-01-29T21:37:05.659-05:00), DataStoreFile(94faee66-ef35-4d00-9d05-ea98db2eafa3,pbsmrtpipe::master.log,PacBio.FileTypes.log,0,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/pbscala-job.stdout,false,Job Master Log,Job Master log of the Import Dataset job), DataStoreFile(8f017810-09fb-481a-9cde-a702fabaa597,pbscala::dataset_report,PacBio.FileTypes.JsonReport,397,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/dataset-reports/simple_dataset_report.json,false,PacBio Report simple_dataset_report,PacBio DataSet Report for simple_dataset_report)))))
[INFO] [2018-01-29T21:37:06.485-05:00] attempting to import
PacBioDataStore Summary 3 files Created at 2018-01-29T21:37:06.485-05:00 Schema version 0.2.1
1. DataStoreFile(36c19ac0-c34b-fc6b-86f2-743a3da771e3,pbscala::import_dataset,PacBio.DataSet.SubreadSet,2410,2018-01-29T21:37:05.659-05:00,2018-01-29T21:37:05.659-05:00,/home/data/pacbio/raw_data/Arabidopsis_data_demo/3_C01_customer/m54113_160914_092411.subreadset.xml,false,pacbio_dataset_subreadset-160923_085639252,Imported DataSet on 2018-01-29T21:37:05.659-05:00)
2. DataStoreFile(94faee66-ef35-4d00-9d05-ea98db2eafa3,pbsmrtpipe::master.log,PacBio.FileTypes.log,0,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/pbscala-job.stdout,false,Job Master Log,Job Master log of the Import Dataset job)
3. DataStoreFile(8f017810-09fb-481a-9cde-a702fabaa597,pbscala::dataset_report,PacBio.FileTypes.JsonReport,397,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/dataset-reports/simple_dataset_report.json,false,PacBio Report simple_dataset_report,PacBio DataSet Report for simple_dataset_report)
[INFO] [2018-01-29T21:37:06.568-05:00] Successfully inserted datastore files:
[INFO] [2018-01-29T21:37:06.568-05:00] Successfully entered SubreadSet SubreadServiceDataSet(-99,36c19ac0-c34b-fc6b-86f2-743a3da771e3,pacbio_dataset_subreadset-160923_085639252,/home/data/pacbio/raw_data/Arabidopsis_data_demo/3_C01_customer/m54113_160914_092411.subreadset.xml,2018-01-29T21:37:06.544-05:00,2018-01-29T21:37:06.544-05:00,573889,5347463396,3.0.1, ,subreadset,9a6026d88580d6130acbbe2d28e98c55,54113,m54113_160914_092411,PacBio_LER0_32kbLibrary_1_3_C01,3_C01,unknown,0,PacBio_LER0_32kbLibrary_1_3_C01,None,37,1,PacBio.DataSet.SubreadSet)
Unsupported DataSet type PacBio.FileTypes.log. Imported DataStoreFile(94faee66-ef35-4d00-9d05-ea98db2eafa3,pbsmrtpipe::master.log,PacBio.FileTypes.log,0,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/pbscala-job.stdout,false,Job Master Log,Job Master log of the Import Dataset job). Skipping extended/detailed importing
Unsupported DataSet type PacBio.FileTypes.JsonReport. Imported DataStoreFile(8f017810-09fb-481a-9cde-a702fabaa597,pbscala::dataset_report,PacBio.FileTypes.JsonReport,397,2018-01-29T21:37:06.485-05:00,2018-01-29T21:37:06.485-05:00,/opt/pacbio/smrtlink/userdata/jobs_root/000/000037/dataset-reports/simple_dataset_report.json,false,PacBio Report simple_dataset_report,PacBio DataSet Report for simple_dataset_report). Skipping extended/detailed importing
letunglam is offline   Reply With Quote
Old 01-30-2018, 07:54 AM   #2
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 318
Default

For a quick resolution, file a ticket with Pacbio tech support.

Alternatively, what version of SMRT Link are you using, and where did the data come from?
rhall is offline   Reply With Quote
Old 01-31-2018, 12:48 AM   #3
letunglam
Junior Member
 
Location: Viet nam

Join Date: Jan 2018
Posts: 3
Default

Quote:
Originally Posted by rhall View Post
For a quick resolution, file a ticket with Pacbio tech support.

Alternatively, what version of SMRT Link are you using, and where did the data come from?
SMRT Link version is 5.01
I get data from pacbio: https://www.pacb.com/blog/sequel-sys...nome-assembly/
letunglam is offline   Reply With Quote
Old 01-31-2018, 02:04 PM   #4
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 318
Default

Can you try on the command line
Code:
pbservice import-dataset --host <hostname> --port <port> m54113_160914_092411.subreadset.xml --verbose
rhall is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:25 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO