SPAdes --restart-from error

Question

[chapmansm13]

Hi,

I've been using SPAdes to assemble, and I tried to restart it from a check point but I got this error:

spades.py --careful --cov-cutoff auto -k 127,85 --restart-from k127 -o /Users/admin/Desktop/Deepseq/39/Spades/

== Error ==  Please specify option (e.g. -1, -2, -s, etc) for the following paths: and, R2/39_S14_L001_R1_001_prinseq_trim, right, 50, trim, qual, 30, both.fastq, R1, and, R2/39_S14_L001_R2_001_prinseq_trim_right_100_trim_qual_30_both.fastq

The two files are my reads, but when I try to specify them it simply says that == Error == you cannot specify reads with --restart-from option!

I'm a little confused as to whats happening and how to specify the options?

Many thanks,
Sarah

[apelin20]

In your command line you are not specifying paths to reads. Where are your reads locates?

[h.mon]

If you are running SPAdes with --continue or --restart-from, one do not need specify input files, they will be read from the previous run logs. However, looking carefully at the error message, it seems SPAdes did not understand filenames, and I guess they contain spaces.

== Error ==  Please specify option (e.g. -1, -2, -s, etc) for the following paths:

and,

R2/39_S14_L001_R1_001_prinseq_trim,

and so forth.

Answer 1

[h.mon]

I think the problem is -k values must be in ascending order, so -k 127,85 is not permitted. Have you tried:

spades.py --restart-from k127 -k 85,127 -o /Users/admin/Desktop/Deepseq/39/Spades/

the -o folder should be the exactly the same from a previous run.

You may also try:

spades.py --continue -o /Users/admin/Desktop/Deepseq/39/Spades/

Edit: Removed space in -k 85,127, there shouldn't be any.

Edit 2: See my comment above, do your read names contain spaces?

[yeissler]

I have the same issue and I tried to solved it as you suggest so I run this from my bin directory:

/Users/laboratoriovirologia/Documents/SPAdes-3.11.1-Darwin/bin/metaspades.py --continue k55 -o /Users/laboratoriovirologia/documents/SPAdes-3.11.1-Darwin/bin/02spades_H3

but I got the same error:

== Error ==  Please specify option (e.g. -1, -2, -s, etc) for the following paths: k55
I also tried specifying the files just as I wrote the command when I started the analysis but adding --continue k55:
/Users/laboratoriovirologia/Documents/SPAdes-3.11.1-Darwin/bin/metaspades.py --continue k55 --pe1-1 /Users/laboratoriovirologia/Documents/SPAdes-3.11.1-Darwin/bin/Mose_8/H3TQ30_forward_paired.fq.gz --pe1-2 /Users/laboratoriovirologia/Documents/SPAdes-3.11.1-Darwin/bin/Mose_8/H3TQ30_reverse_paired.fq.gz -o /Users/laboratoriovirologia/documents/SPAdes-3.11.1-Darwin/bin/02spades_H3

I got the same error: == Error == Please specify option (e.g. -1, -2, -s, etc) for the following paths: k55

I am in a loop, also tried just to write -o 02spades_H3 without the pwd and same error.

What could be the problem?