rvalieris parallel-fastq-dump issues

rvalieris / parallel-fastq-dump

parallel fastq-dump wrapper

MIT License

263 stars 33 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

no parallelize with snakemake

#56 Fadwa7 opened 5 months ago
4
IndexError: sra-stat output parsing error!

#55 Naturalist1986 opened 6 months ago
3
IndexError

#54 Kiliankleemann closed 5 months ago
5
SRA Lite

#53 moqri opened 10 months ago
1
Parallel-fastq-dump has been running for nearly 24 hours

#52 ZhangMH2000 closed 1 year ago
12
The dependency sra-tools in conda is outdated and will trigger errors

#51 DongzeHE closed 1 year ago
3
Error message appear after running

#50 kubotakehiro closed 1 year ago
2
can't install parallel-fastq-dump

#49 dmncyap closed 1 year ago
1
fastq-dump.2.11.0 err: storage exhausted while writing...

#48 mike2vandy closed 1 year ago
2
parallel-fastq-dump not working any more

#47 FarmOmics closed 1 year ago
16
Upgrade to sra toolkit 3.0

#46 marina-yurieva closed 1 year ago
1
include-technical reads for single cell studies

#45 MEFarhadieh closed 2 years ago
7
Is this expected to be faster than fasterq-dump as well?

#44 achillesrasquinha opened 2 years ago
2
What does it mean if -split-files is used but I still only get a single output file for each input file?

#43 joepalermo closed 2 years ago
2
How are files named in the output of parallel-fastq-dump?

#42 yls2g13 closed 2 years ago
1
Benchmark comparison

#41 Midnighter opened 2 years ago
11
Download all reads for given experiment accession

#40 snayfach closed 2 years ago
5
it never ends...

#39 sunnlife1978 closed 3 years ago
1
IndexError

#38 nrclaudio closed 3 years ago
7
better error reporting for sra-stat

#37 nick-youngblut closed 3 years ago
2
IndexError: list index out of range

#36 nick-youngblut closed 3 years ago
2
FileNotFoundError: [Errno 2] No such file or directory:

#35 nick-youngblut closed 3 years ago
2
an integer is required (got type _io.BufferedWriter)

#34 Divyoj-Singh closed 3 years ago
2
Explicitly close the file descriptors

#33 nh13 closed 3 years ago
0
fastq-dump uses network even though I prefectech

#32 nh13 closed 3 years ago
3
Forward and reverse identifier /1 and /2

#31 smb20200615 closed 3 years ago
4
Unknown error

#30 azzaea closed 3 years ago
2
Question about using parallel fastqdump with prefetch

#29 smb20200615 closed 3 years ago
10
wrong file size of output fastq files

#28 millerh1 closed 4 years ago
2
TemporaryDirectory error

#27 dgiovannelli closed 4 years ago
1
Something writes to root, even if tmpdir is defined.

#26 joachimwolff closed 4 years ago
1
IndexError: list index out of range

#25 Maarten-vd-Sande closed 4 years ago
6
Failed to retrieve results error

#24 JonathonMifsud closed 4 years ago
4
query unauthorized while resolving query within virtual file

#23 Kapeel closed 4 years ago
3
OSError: [Errno 39] Directory not empty: '2'

#22 arglatha closed 4 years ago
1
downloads are slower if maxSpotId is set higher than n_spots

#21 hgbrian closed 5 years ago
1
support -N/--minSpotId and -X/--maxSpotId

#20 kfuku52 closed 5 years ago
3
storage exhausted while writing file within file system module

#19 PhilPalmer closed 5 years ago
4
superslow

#18 antonkulaga closed 5 years ago
3
how to dealwith downloaded sra file

#17 zyxplus closed 5 years ago
6
AttributeError: 'module' object has no attribute 'TemporaryDirectory'

#16 royfrancis closed 6 years ago
1
does it work with the -Z option?

#15 dtenenba closed 5 years ago
1
point to a local file?

#14 Sames-Jtudd closed 6 years ago
3
Conflicting environment

#13 thuang41 closed 6 years ago
1
conda install failed on MacOS X Yosemite 10.10.5

#12 weihua77 closed 6 years ago
1
Cannot find temporary files

#11 devmon closed 6 years ago
5
exception: No such file or directory: 'sra-stat'

#10 dtenenba closed 6 years ago
1
temp file attribute error

#9 slschnorr closed 6 years ago
5
can't seem to install with conda install

#8 adeslatt closed 6 years ago
1
Problem running parallel-fastq-dump on a cluster

#7 samuelCollombet closed 6 years ago
1