Your message dated Fri, 2 Sep 2016 09:20:36 +0200 with message-id <[email protected]> and subject line Re: [ncbi/sra-tools] does not load data from fastq files to directory (#39) has caused the Debian Bug report #824402, regarding sra-toolkit: does not load data from fastq files to directory (and probably more problems) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 824402: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=824402 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: sra-toolkit Version: 2.3.5-2+dfsg-1 Severity: grave Justification: renders package unusable Dear Maintainer, The latf-load binary from sra-toolkit package doesn't load data from fastq files to directory - it will ends up with these errors: $ latf-load -q PHRED_33 -o Desktop/test Desktop/test.fastq 2016-05-15T13:51:17 latf-load.2.3.5 warn: Deprecated argument '-q' may not be supported in future releases. Please use '--quality' instead. 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - file="align/align.vschema" 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - failed to parse schema file align/align.vschema 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - accession="test" errors="0" status="failure" 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory within file system module - load failed It seems the binary doesn't see the necessary vschema files. There is everything fine on the upstream package. The temporary solution is to copy/symlink schema directory from upstream package (latest version) to /usr - this works fine. I think the problem influence other binaries too, but I don't know - didn't try. I tryed this on the clean Debian 8 installation - the problem remains. -- System Information: Debian Release: 8.4 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: i386 (i686) Kernel: Linux 3.16.0-4-686-pae (SMP w/1 CPU core) Locale: LANG=sk_SK.UTF-8, LC_CTYPE=sk_SK.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages sra-toolkit depends on: ii libbz2-1.0 1.0.6-7+b3 ii libc6 2.19-18+deb8u4 ii libxml2 2.9.1+dfsg1-5+deb8u1 ii sra-toolkit-libs0 2.3.5-2+dfsg-1 ii zlib1g 1:1.2.8.dfsg-2+b1 sra-toolkit recommends no packages. sra-toolkit suggests no packages. -- no debconf information
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--- Begin Message ---Hi, On Thu, Sep 01, 2016 at 11:55:22AM -0700, Anatoly Boshkin wrote: > Yes, but in this particular case the loader fails to parse the tagline. > Our FASTQ tag line parser has been built based on real submissions and one of > its features is extraction of certain data (spot names, read groups, read > numbers) from a multitude of variations on the FASTQ format that NCBI has to > deal with. As such, even though the tagline parsing rules are somewhat loose, > it is not a free format. > In your test's tagline, white space is what causes the failure. Please try > replacing spaces with underscores. I can confirm that replacing spaces by underscores in /usr/share/doc/python-biopython-doc/Tests/Quality/sanger_93.fastq solved the issue and the file can be easily loaded. I have tested a couple of other fastq files successfully (with one exception where removing a space has helped. While I think there could be some enhancement regarding the error message ("syntax error, unexpected fqWS" is a bit weak in my personal opinion) I'm hereby closing the Debian bug report which was about not found vschema files anyway. Jana, please test the new version of sra-toolkit thoroughly and keep on reporting bugs. Kind regards Andreas. -- http://fam-tille.de
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