"Status (0 is good): 0[1,0,...0]

[jdarias93]

Hi Norgal Team,

I am trying to run Norgal with forward and reverse fastq files, but I either get the following failure message or the program just keeps running indefinitely without update:

$ python norgal.py -i LeDul_PairedUnusedReads_PostChloroEx1.fastq LeDul_PairedUnusedReads_PostChloroEx2.fastq -o LeDul_Norgal --blast Namespace(b=10, blast=True, c=None, delete=False, e=0.0001, i=['LeDul_PairedUnusedReads_PostChloroEx1.fastq', 'LeDul_PairedUnusedReads_PostChloroEx2.fastq'], m=10000, o=['LeDul_Norgal'], r=None, t=2, trim=False) [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 0 ########### ln -s /Users/amandafisher/Desktop/Josh-Inbox/src/LeDul_PairedUnusedReads_PostChloroEx1.fastq reads/trim1.fq; ln -s /Users/amandafisher/Desktop/Josh-Inbox/src/LeDul_PairedUnusedReads_PostChloroEx2.fastq reads/trim2.fq Status (0 is good): 0[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 1 Command '/Users/amandafisher/Desktop/Josh-Inbox/src/binaries/darwin/megahit -1 reads/trim1.fq -2 reads/trim2.fq --k-list 21,49,77,105 -t 2 -o assemblies/initial --mem-flag 0' returned non-zero exit status 1 ****** Failed Assembling all reads for ND determination.. Exit.

Please let me know if you require any other information. Thank you.

[row-kristopher]

I am also getting this error.

any luck with a troubleshoot?

[jdarias93]

Hi @row-kristopher

I used another program that does the same thing: https://github.com/chloroExtractorTeam/chloroExtractor

It is pretty user-friendly and effective. You just need to set it up through Docker. All the instructions are on the Github page.