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Andrew Klymenko edited this page Oct 6, 2015 · 14 revisions

We receive email just about every day with a problem report. These generally fall into a small handful of categories, so today we will start posting some as generalized questions and answers.

Nearly all questions involve the use of fastq-dump.

  1. "I’m trying to convert sra file to fastq using fast-dump in sratoolkit.2.3.1, but error reported like:
    fastq-dump.2.3.1 err: manager not found while constructing path within virtual file system module - failed"

  2. fastq-dump.2.4.2 err: name not found while resolving tree within virtual file system module - failed SRR1237957.sra

  3. fastq-dump.2.4.3 err: data corrupt while executing function within virtual database module - failed SRR1449308

***Resolving a common problem with decryption of dbGaP data:

  1. I am trying to decrypt some files a dbGaP project and it does not work

I’m trying to convert sra file to fastq using fast-dump in sratoolkit.2.3.1, but error reported like:
fastq-dump.2.3.1 err: manager not found while constructing path within virtual file system module - failed

The first clue to a problem comes from the tool version. In this case, version 2.3.1 is reporting the problem. We released that on March 5, 2013. Any tools older than 6 months may not work on newer runs. You should always download the latest version as your first step.

The reason for this is that the tools found in the SRA Toolkit contain code that would traditionally run within a server somewhere inside NCBI. This provides enormous scalability and is one of the reasons the SRA is able to grow at the rates it does. But since the SRA itself is a living, evolving entity, we need to continually update our tools.

2015-02-04T05:46:00 fastq-dump.2.4.2 err: name not found while resolving tree within virtual file system module - failed SRR1237957.sra.
I've searched on google to see if there was anyone who had the same issue, but couldn't find one. And I tried in couple different computer settings and servers and none of them seemed to solve the problem.

SRA Toolkit log reports can seem cryptic. This is because most of the text is auto-generated from a 32-bit 5-field code. (We hope to improve readability in the future!)

In this case we see that the resolver could not locate the object named SRR1237957**.sra** (notice the extension). When the resolver sees a simple accession with the .sra extension, it is treated as a file name in the current working directory. You should use the accession without any extension, or else give a path to the run file if already manually downloaded. See vdb name resolution for an in-depth description.

fastq-dump.2.4.3 err: data corrupt while executing function within virtual database module - failed SRR1449308
There was a bug introduced in our networking code that caused us to lose notification of a dropped connection. The result was an attempt to read an empty blob, which in turn resulted in decompression code saying that it was seeing bad data.

In reality, there is nothing wrong with the data, only the retrieval. Get version 2.4.4 instead.

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