Last updated:2015.4.28.

FAQ

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FAQs 29 : Tag = pipeline
I have a DRA account, but I can’t log in to Pipeline Pipeline
In order to use DDBJ Pipeline, you need a Pipeline-exclusive account, separate from your DRA account. We are sorry for the extra trouble, but please proceed to “create new account” from the log-in page, and acquire a new Pipeline account.
Last Updated:September 16, 2014
I have registered my new account, but I’m not receiving e-mails. Pipeline
Normally, you would receive an e-mail from ( pipeline_dev@ddbj.nig.ac.jp ) with your Login ID and Password within a few minutes. If it seems that you haven’t received this e-mail, please check the filter settings on your e-mail software. There is also the possibility that the registered e-mail address is not correct; once you have kindly confirmed this e-mail address, please try to register your account again.
Last Updated:September 16, 2014
My FTP connection is not good Pipeline
Case 1. DRA users

There are cases where DRA registered users cannot connect to FTP. When this occurs, if you log in to Pipeline, and change your password, FTP connection will be possible.

Case 2. FTP client is not responding

It is not possible for Pipeline to connect to FTP with an FTP client that is provided as standard on Windows and MAC.
An FTP over SSL server is used for Pipeline, and FTP log-in, as well as sending and receiving data, is encrypted; a client that can handle to this is necessary to use FTP.
For Windows, WinSCP, and for MAC, Cyberduck, can handle the above-mentioned connection.

WinSCP
http://winscp.net/
Cyberduck
http://cyberduck.ch/
  
Last Updated:September 16, 2014
On HTTP upload, the files are not displayed in a list Pipeline
For HTTP transmission, uploading takes time. In some cases transmission may be abandoned/disconnected before completion.

Furthermore, even once the files have been uploaded, sometimes the list is not updated; please re-load the page.
Last Updated:September 16, 2014
It’s taking a long time to run jobs, does this mean there is a problem? Pipeline
If you are running denovoAssembly, (Velvet in particular) you may need several days for processing completion.

In most cases the processing time will be stretched proportional to the data load to be processed, but depending on the setting method in Options, the quality of the original data etc., processing may not be completed at all. In this situation, it’s most likely that the job has been hung-up, and since left as it is, this would cause resources to be wastefully monopolized, we may force quit on our side.
Last Updated:September 16, 2014
My job generated an error Pipeline
( Pattern 1 )
If on the Status screen, the Status shows as “error” and the Start time as “not displayed”.
  • This error means that something has caused an inability to load he specified query files.
  • Please confirm that the specified query files are text files. (There are no particular specified filename extensions.)
  • Then confirm that there are no problems with the format of FASTA/FASTQ etc.
  • Please note that if there are blank lines (as final lines etc.) included, an error will be generated.
  • Please confirm that the filenames are in single-byte Roman letters (symbols). (Double-byte characters, in Japanese etc., are not handled)
  • Please check that there are no spaces in the filenames.
  • If you have selected Assembly→BLAT(mapping), and have not been able to obtain the Assembly results file, on BLAT(mapping) this status will occur.

FAQ_2_1e_1
( Pattern 2 )
If on the Status screen, the Status shows as “error” and the Start time as “displayed”.
  • Confirm that there are no problems with the format of FASTA/FASTQ etc. for the specified query files.
  • Please check the logical input value in Options etc.
  • From the Selecting Tools screen, you can refer to each Tool’s site, or Help. ※ Depending on the tool selected, there may be a maximum line length restriction.
  • On the Detail view screen, there are cases where the cause can be specified from the Command being run and the Log1 (standard output) and Log 2 (standard error); please check this.

( Pattern 3 )
If on the Status screen, the Status shows as “complete” and there is an error shown on the Detail view screen.
  • Please check the logical input value in Options etc.
  • From the Selecting Tools screen, you can refer to each Tool’s site, or Help. ※ Depending on the tool selected, there may be a maximum line length restriction.
  • On the Detail view screen, there are cases where the cause can be specified from the Command being run and the Log1 (standard output) and Log 2 (standard error); please check this.

FAQ_1_3e_1
If you cannot specify the cause, or if you would like to make a comment, please kindly contact support(pipeline_dev@ddbj.nig.ac.jp).
Last Updated:January 8, 2015
I can’t change the parameters (options) for the tools to be run. Pipeline
On the Tool Selection screen, there are links to the manual pages of each tool. Please read these, and then on the Setting for Assembly/Mapping screen, set the appropriate parameters in the blank box underneath Set optional parameters.
Last Updated:October 24, 2014
Can I delete the fields registered in User original sets? Pipeline
Currently we aren’t handling this, but we will raise it as a system improvement proposal.
Last Updated:October 24, 2014
Are the files generated in mapping only SAM files, and does generation of BAM files have to be executed separately with SAMTools? Pipeline
SAMTools is also programmed, so BAM files can be created too.
Last Updated:October 24, 2014
With the current functions of Pipeline, can SNP extraction not be carried out using varFilter? Pipeline
You can use mpileup for this.
Last Updated:October 27, 2014
Can I download SAMtools index files? Pipeline
We will look into handling this.
Last Updated:October 27, 2014
What happens if you select Uniq in Step 3 of Set optional parameters? Pipeline
From the lines showing the mapping results of the individual Reads within the SAM files, only lines with results where one area was mapped in a genome (including XT:A:U) are output (only BWA is handled). Please refer to the below. http://seqanswers.com/forums/showthread.php?t=5450
Last Updated:October 27, 2014
I don’t know the difference between SAMtools pileup and SAMtools mpileup. Pipeline
Mpileup is pileup with SNP calling added. Please refer to the below.
http://samtools.sourceforge.net/mpileup.shtml
Last Updated:October 27, 2014
Is out.sam SAM file generation for mapping information? Pipeline
It’s the generation results.
Last Updated:October 27, 2014
With the command samtools view -bS -o out.bam out.sam, will SAM--->BAM conversion occur? Pipeline
samtools view is a command which outputs, from the results mapped onto the reference sequence (genome), only the results from a specified domain. However, basically this is not permitted, so it will be all the reference sequence (genome) results.
http://samtools.sourceforge.net/samtools.shtml#3
Last Updated:October 27, 2014
With the command samtools sort out.bam out2, will there be BAM sorting, and an output format of out2.srt.bam? Pipeline
It will be downloaded as out2.bam.zip, and when you decompress this file, it will become out2.bam.
Last Updated:October 27, 2014
I don’t know what kind of files samtools view –hX out.bam>out.sam and merged SAM are. Pipeline
Merged.sam is likely to be the files within the framework of “Download merged pileup file” from the Detail view screen, but this is the results of sam per chromosome, combined into one.
out.samX
samtools view -hX
Usage: samtools view [options]|[region1 [...]]
Options: -h     print header for the SAM output
            -X     output FLAG in string (samtools-C specific) 

For sam and samX, the 2nd column inscription changes. Please refer to the below.
http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ#The_integer_FLAG_field_is_not_friendly_to_eyes
Merged SAM, if there is one chromosome, has the same contents as out.sam (but the Download files are compressed).
Last Updated:October 27, 2014
Is out2.bam a sorted BAM file? Pipeline
Yes
Last Updated:October 27, 2014
The files that I uploaded using FTP are not reflected on the Web. Pipeline
Files uploaded to the FTP server are automatically transferred to a specific directory on the National Institute of Genetics (NIG) supercomputer after the upload is complete. Thus, it is normal for files to appear to have vanished after uploading.
Last Updated:April 28, 2015
The Delete button shown at the upper left of the [Job Status window] does not do anything. Also, I want to change the displayed file name. Pipeline
The function of the Delete key is currently disabled. This is because it is useful for development purposes to be able to refer to the execution records of jobs, even if the job failed. If you wish to delete those records nonetheless, we will do it for you; please contact us. (pipeline_dev@ddbj.nig.ac.jp) In general, it is not possible to change a submission accession that you have previously specified. If you wish to change the name of the file corresponding to a job, we will delete the job itself. Then you can use the procedure following file upload to specify a different name for Study Title.
Last Updated:April 28, 2015
I entered an accession number that is shown in the DRA Search display in the [Import Public DRA tab], but I got an error message saying that the number was not found. Pipeline
Within Pipeline, the displayed list of accession numbers is obtained from the list released by NCBI. This list may differ in some places from the list released by DDBJ. If you receive an error message saying that the item in question was not found, please contact us. We will take care of the problem. (pipeline_dev@ddbj.nig.ac.jp)
Last Updated:April 28, 2015
Data registered for DRA under the [Import Public DRA tab] cannot be imported. Pipeline
From the “Import Public DRA”, tab it is possible to select data that have already been released by DRA; however, at present, the system is not equipped with functionality to fetch unreleased data, even data previously registered within DRA, into Pipeline. We regret this inconvenience; please use FTP to upload the data to the Pipeline server, separately from DRA.
Last Updated:April 28, 2015
The Preprocessing step completed without any problems, but the resulting file has size 0 kb Pipeline
This is probably caused by an incorrect format specification for the Quality Score during execution of the Preprocessing step. Check the content of your query file and make sure that phred33 or phred64 is specified.
Last Updated:April 28, 2015
Are there any conventions in place for specifying file names or other parameters when performing the Preprocessing step? Pipeline
When uploading files, for paired-end, use the designations _1 and _2 at the end of the base file name (that is, just before the file extension) to distinguish the files.
Last Updated:April 28, 2015
I do not know how to fill out the blank input fields in the [Set Optional Parameters window]. Pipeline
Please read the manual for the tool that you have selected and configure all relevant options (for options that may be set to default values, leave the corresponding input fields blank). Entering any text other than option values will lead to run-time errors.
Last Updated:April 28, 2015
How do I send data currently stored on the DDBJ supercomputer to Pipeline? Similarly, how do I send data to the supercomputer after the Pipeline analysis? Pipeline
To upload data from the supercomputer to Pipeline, use the ftp command from the supercomputer to connect to the DDBJ Pipeline FTP server; this allows you to transfer data directly without going through your local computer. More specifically, the procedure is as follows. 1. After logging in to the gw supercomputer, use qlogin to move to one of the computational nodes. 2. Use the ftp command to connect to the server: $ ftp pdata.nig.ac.jp 3. When prompted, enter the DDBJ Pipeline user name and password. 4. Once you are connected, upload your files to the directory named query. After you have uploaded files, you may register them within Pipeline by following procedures similar to that used in the GUI. For the reverse process—copying result files to the supercomputer—at present, there is no way to do this. (However, it is possible to copy result files individually by specifying a destination location and assigning it write privileges.) As the question suggests, it would certainly be convenient if file transfers between the supercomputer and Pipeline could be carried out directly; this is a goal of future development efforts.
Last Updated:April 28, 2015
Our company would like to use Pipeline for commercial purposes. May we do so? If so, will the confidentiality of sequence information be guaranteed? Pipeline
There is nothing wrong with using DDBJ Pipeline for research and development purposes. However, please refrain from routinely incorporating the service into commercial endeavors, such as analyses that your company may be hired to perform on a contract basis. Regarding security, your data cannot be seen by other users; however, note with caution that other users will be able to see file names unless you rename them using the GUI settings. In addition, results are subject to volume restrictions and are deleted after 60 days. After this time period, you must repeat the analysis.
Last Updated:April 28, 2015
Is it possible to perform assemblies involving combinations of single-end and paired-end data from Illumina or Roche454? Pipeline
Tools supporting hybrid assembly, such as Velvet and ABySS, do exist; however, at present, Pipeline is not equipped with functionality to specify two types of reads, and thus hybrid assemblies may not be performed.
Last Updated:April 28, 2015
This question pertains to the BWA uniq option in the [Set Optional Parameters window]. What are the differences between the four possible choices for “Please choose uniq mode.”? Pipeline
  1. Do not remove any read. Do not take any steps to ensure uniqueness.
  2. Retain pairs when both reads mapped uniquely or one of reads mapped uniquely, and Discard other pairs. Retain a pair if either one or both of the two reads mapped uniquely. (The pair will be discarded if both reads yielded multiple hits.)
  3. Retain pairs when both reads mapped uniquely, and Discard other pairs. Retain a pair only if both reads mapped uniquely. (The pair will be discarded if either or both of the reads yielded multiple hits.)
  4. Retain uniquely mapped reads and discard multiply mapped reads. Retain only uniquely mapped reads irrespective of pairing. The optimal setting for this option depends on the circumstances, but option 3 is the most stringent, option 2 is the most lenient, and option 4 is somewhat intermediate between these two options.
Last Updated:April 28, 2015
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