rvalieris/parallel-fastq-dump issues and pull requests

#57 - fastq-dump error! exit code: 3

Issue - State: open - Opened by binbinL 2 months ago - 1 comment

#56 - no parallelize with snakemake

Issue - State: open - Opened by Fadwa7 8 months ago - 4 comments

#55 - IndexError: sra-stat output parsing error!

Issue - State: open - Opened by Naturalist1986 9 months ago - 3 comments

#54 - IndexError

Issue - State: closed - Opened by Kiliankleemann about 1 year ago - 5 comments

#53 - SRA Lite

Issue - State: open - Opened by moqri about 1 year ago - 1 comment
Labels: question

#52 - Parallel-fastq-dump has been running for nearly 24 hours

Issue - State: closed - Opened by ZhangMH2000 over 1 year ago - 12 comments

#51 - The dependency sra-tools in conda is outdated and will trigger errors

Issue - State: closed - Opened by DongzeHE over 1 year ago - 3 comments

#50 - Error message appear after running

Issue - State: closed - Opened by kubotakehiro almost 2 years ago - 2 comments

#49 - can't install parallel-fastq-dump

Issue - State: closed - Opened by dmncyap almost 2 years ago - 1 comment

#48 - fastq-dump.2.11.0 err: storage exhausted while writing...

Issue - State: closed - Opened by mike2vandy about 2 years ago - 2 comments

#47 - parallel-fastq-dump not working any more

Issue - State: closed - Opened by FarmOmics about 2 years ago - 16 comments

#46 - Upgrade to sra toolkit 3.0

Issue - State: closed - Opened by marina-yurieva over 2 years ago - 1 comment

#45 - include-technical reads for single cell studies

Issue - State: closed - Opened by MEFarhadieh over 2 years ago - 7 comments

#44 - Is this expected to be faster than fasterq-dump as well?

Issue - State: open - Opened by achillesrasquinha almost 3 years ago - 2 comments
Labels: question

#43 - What does it mean if -split-files is used but I still only get a single output file for each input file?

Issue - State: closed - Opened by joepalermo almost 3 years ago - 2 comments

#42 - How are files named in the output of parallel-fastq-dump?

Issue - State: closed - Opened by yls2g13 almost 3 years ago - 1 comment

#41 - Benchmark comparison

Issue - State: open - Opened by Midnighter about 3 years ago - 11 comments

#40 - Download all reads for given experiment accession

Issue - State: closed - Opened by snayfach over 3 years ago - 5 comments

#39 - it never ends...

Issue - State: closed - Opened by sunnlife1978 over 3 years ago - 1 comment

#38 - IndexError

Issue - State: closed - Opened by nrclaudio over 3 years ago - 7 comments

#37 - better error reporting for sra-stat

Pull Request - State: closed - Opened by nick-youngblut over 3 years ago - 2 comments

#36 - IndexError: list index out of range

Issue - State: closed - Opened by nick-youngblut over 3 years ago - 2 comments

#35 - FileNotFoundError: [Errno 2] No such file or directory:

Issue - State: closed - Opened by nick-youngblut over 3 years ago - 2 comments

#34 - an integer is required (got type _io.BufferedWriter)

Issue - State: closed - Opened by Divyoj-Singh over 3 years ago - 2 comments
Labels: bug

#33 - Explicitly close the file descriptors

Pull Request - State: closed - Opened by nh13 over 3 years ago

#32 - fastq-dump uses network even though I prefectech

Issue - State: closed - Opened by nh13 over 3 years ago - 3 comments

#31 - Forward and reverse identifier /1 and /2

Issue - State: closed - Opened by smb20200615 over 3 years ago - 4 comments

#30 - Unknown error

Issue - State: closed - Opened by azzaea almost 4 years ago - 2 comments

#29 - Question about using parallel fastqdump with prefetch

Issue - State: closed - Opened by smb20200615 almost 4 years ago - 10 comments

#28 - wrong file size of output fastq files

Issue - State: closed - Opened by millerh1 over 4 years ago - 2 comments

#27 - TemporaryDirectory error

Issue - State: closed - Opened by dgiovannelli over 4 years ago - 1 comment

#26 - Something writes to root, even if tmpdir is defined.

Issue - State: closed - Opened by joachimwolff over 4 years ago - 1 comment

#25 - IndexError: list index out of range

Issue - State: closed - Opened by Maarten-vd-Sande over 4 years ago - 6 comments

#24 - Failed to retrieve results error

Issue - State: closed - Opened by JonathonMifsud about 5 years ago - 4 comments

#23 - query unauthorized while resolving query within virtual file

Issue - State: closed - Opened by Kapeel about 5 years ago - 3 comments

#22 - OSError: [Errno 39] Directory not empty: '2'

Issue - State: closed - Opened by arglatha about 5 years ago - 1 comment

#21 - downloads are slower if maxSpotId is set higher than n_spots

Issue - State: closed - Opened by hgbrian over 5 years ago - 1 comment

#20 - support -N/--minSpotId and -X/--maxSpotId

Pull Request - State: closed - Opened by kfuku52 over 5 years ago - 3 comments

#19 - storage exhausted while writing file within file system module

Issue - State: closed - Opened by PhilPalmer over 5 years ago - 4 comments

#18 - superslow

Issue - State: closed - Opened by antonkulaga about 6 years ago - 3 comments

#17 - how to dealwith downloaded sra file

Issue - State: closed - Opened by zyxplus about 6 years ago - 6 comments

#16 - AttributeError: 'module' object has no attribute 'TemporaryDirectory'

Issue - State: closed - Opened by royfrancis over 6 years ago - 1 comment

#15 - does it work with the -Z option?

Issue - State: closed - Opened by dtenenba over 6 years ago - 1 comment

#14 - point to a local file?

Issue - State: closed - Opened by Sames-Jtudd over 6 years ago - 3 comments

#13 - Conflicting environment

Issue - State: closed - Opened by thuang41 over 6 years ago - 1 comment

#12 - conda install failed on MacOS X Yosemite 10.10.5

Issue - State: closed - Opened by weihua77 over 6 years ago - 1 comment

#11 - Cannot find temporary files

Issue - State: closed - Opened by devmon over 6 years ago - 5 comments
Labels: bug

#10 - exception: No such file or directory: 'sra-stat'

Issue - State: closed - Opened by dtenenba over 6 years ago - 1 comment

#9 - temp file attribute error

Issue - State: closed - Opened by slschnorr over 6 years ago - 5 comments

#8 - can't seem to install with conda install

Issue - State: closed - Opened by adeslatt almost 7 years ago - 1 comment

#7 - Problem running parallel-fastq-dump on a cluster

Issue - State: closed - Opened by samuelCollombet almost 7 years ago - 1 comment

#6 - Can it deal with local sra file?

Issue - State: closed - Opened by shenweima almost 7 years ago - 1 comment

#5 - parallel-fastq-dump can't download some old datasets

Issue - State: closed - Opened by golobor almost 7 years ago - 2 comments
Labels: bug

#4 - Multiple SRA to FASTQ conversion issue

Issue - State: closed - Opened by langouec almost 7 years ago - 2 comments

#3 - Problem installing in Linux

Issue - State: closed - Opened by nuno-agostinho about 7 years ago - 2 comments

#2 - Problem with large files

Issue - State: closed - Opened by apredeus over 7 years ago - 3 comments

#1 - Usage

Issue - State: closed - Opened by TripelB over 7 years ago - 3 comments

GitHub / rvalieris/parallel-fastq-dump issues and pull requests