Same error is still occuring.
• 0 views
•
link
written
by
inaciogmedeiros •
Doubt about specifying options in SPAdes
I've tried to run SPAdes with following command:
$ spades/bin/spades.py -s input.fastq --iontorrent --only-assembler --careful -o output.result
However, following error message occurs:
== Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: /data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq, :
In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru or report an issue on our GitHub repository github.com/ablab/spades Please provide us with params.txt and spades.log files from the output directory.
My questions are:
- I have setted "s" flag (see "-s input.fastq") (it's a single-ended fastq file). Why does still SPAdes gives this error?
- Which is the correct manner, in this case, to run SPAdes?
• 4,606 views
•
link
written
by
inaciogmedeiros •
1 answer
Try:
spades.py --s1 input.fastq ... <other options="">
• 0 views
•
link
written
by
maxwhjohn1988
Log in to answer this question.
More posts like this
-
How to run Spades with debug option
written by marongiu.luigi
-
unicycler error : [Errno 13] Permission denied:
written by jiyoung •
-
SAPdes not support single-end data?
written by zhangdengwei
-
solution for SPades to assemble genome with low quality data
written by StudentBio •
-
SPAdes assembler-Error code 255
written by Menia_gavr •
-
Spades error code 6
written by imdad.ce07buet •
-
MetaSpades can't access memory? Crashes when requesting 45 Gigs on a 128 Gig RHEL6 machine
written by jnowacki
-
rnaSPADES, assembly problems
written by leonardomajul •
-
Denovo assembly of Putative Plasmid
written by jigarnt •
-
How to assemble the bacterial genome; spades
written by dogdif •
The input looks OK. Which SPAdes version are you using?
The version I am using is 3.11.0.
An additional detail: argument for
--s1is a absolute path for input.fastq. Does this make any substantial difference?spades script is also being called via absolute path, from another external path from spades.
As long as the paths are correct, it should not matter if they are relative or full.
Why the error message complains about
/data/home/inacio/V3/missions/reproduce_pipeline_of_wyndemberg/sample_a_trimmed_fastx_trimmer_result.fastq, if you use just-s input.fastq?Command I've posted was a "model" of how I'm using SPAdes (I've ended up forgetting to adapt error message, sorry).
And what is the output of: