Question: Getting Paired end SRA
0
gravatar for ovariohisterectomia
10 months ago by
ovariohisterectomia20 wrote:

Hi everyone, i have a "short" doubt

i want to work with these sequences

https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP131874&o=acc_s%3Aa

I have downloaded 4 samples, but , as it is paired end, i was waiting to get 8 samples (1 forward, and 1 reverse per sample)

Im i doing something wrong?

i have downloaded from here the Accesion List

https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP131874&o=acc_s%3Aa&s=SRR6657766,SRR6657767,SRR6657768,SRR6657769

Then i performed this

prefetch --option-file SraAccList.txt

and this is the output

(base) isma@isma-X455LJ:~$ prefetch --option-file tabla.txt

2020-01-18T16:36:22 prefetch.2.9.3: 1) Downloading 'SRR6657766'...
2020-01-18T16:36:22 prefetch.2.9.3:  Downloading via https...
2020-01-18T16:37:36 prefetch.2.9.3: 1) 'SRR6657766' was downloaded successfully
2020-01-18T16:37:36 prefetch.2.9.3: 'SRR6657766' has 0 unresolved dependencies

2020-01-18T16:37:37 prefetch.2.9.3: 2) Downloading 'SRR6657767'...
2020-01-18T16:37:37 prefetch.2.9.3:  Downloading via https...
2020-01-18T16:39:07 prefetch.2.9.3: 2) 'SRR6657767' was downloaded successfully
2020-01-18T16:39:07 prefetch.2.9.3: 'SRR6657767' has 0 unresolved dependencies

2020-01-18T16:39:09 prefetch.2.9.3: 3) Downloading 'SRR6657768'...
2020-01-18T16:39:09 prefetch.2.9.3:  Downloading via https...
2020-01-18T16:40:26 prefetch.2.9.3: 3) 'SRR6657768' was downloaded successfully
2020-01-18T16:40:26 prefetch.2.9.3: 'SRR6657768' has 0 unresolved dependencies

2020-01-18T16:40:27 prefetch.2.9.3: 4) Downloading 'SRR6657769'...
2020-01-18T16:40:27 prefetch.2.9.3:  Downloading via https...
2020-01-18T16:41:32 prefetch.2.9.3: 4) 'SRR6657769' was downloaded successfully
2020-01-18T16:41:32 prefetch.2.9.3: 'SRR6657769' has 0 unresolved dependencies

After that i performed this, and then the output (im showing you just One, for example, the others say the same)

fastq-dump –X 5 –Z –split-files SRR6657766.sra

and then the output

020-01-18T16:52:13 fastq-dump.2.9.3 err: libs/vfs/manager.c:1904:VFSManagerOpenDirectoryReadKfs: item not found while constructing within virtual database module - the path '–X' cannot be opened as database or tab
2020-01-18T16:52:13 fastq-dump.2.9.3 err: libs/vfs/manager.c:1904:VFSManagerOpenDirectoryReadKfs: item not found while constructing within virtual database module - the path '5' cannot be opened as database or table
2020-01-18T16:52:13 fastq-dump.2.9.3 err: libs/vfs/manager.c:1904:VFSManagerOpenDirectoryReadKfs: item not found while constructing within virtual database module - the path '–Z' cannot be opened as database or tab
2020-01-18T16:52:13 fastq-dump.2.9.3 err: libs/vfs/manager.c:1904:VFSManagerOpenDirectoryReadKfs: item not found while constructing within virtual database module - the path '–split-files' cannot be opened as database or tab
Read 4157590 spots for SRR6657766.sra
Written 4157590 spots for SRR6657766.sra
Read 4157590 spots total
Written 4157590 spots total

I think the last command is the problem, but i cannot find it...would appreciate your help!

Thank you so much.

rna-seq • 377 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by ovariohisterectomia20
0
gravatar for ovariohisterectomia
10 months ago by
ovariohisterectomia20 wrote:

Im so sorry for this, i made a mistake because the right command is

fastq-dump --split-files SRR6657767.sra

Then i got 2 fastq files...

so sorry

SOLVED

ADD COMMENTlink written 10 months ago by ovariohisterectomia20

No problem, happens to all of us :)

For completeness, if you get tired of fastq-dump you can get fastq directly from ENA, see Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD REPLYlink modified 10 months ago • written 10 months ago by ATpoint42k
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