Closed YuyaKiguchi closed 2 years ago
Thank you for reporting. I have fixed the image in DockerHub.
As a command, you will need to specify file names with /data .
docker run -v $PWD:/data --rm rkajitani/metaplatanus metaplatanus -IP1 /data/R1.fastq.gz /data/R2.fastq.gz -p /data/pacbio.fasta --o out -t 50 > log 2>&1
I hope you re-pull the docker image and try the command above.
Sorry for bothering you.
I had the same error with the conda installation. Which is metaplatanus v1.3.0
Thanks for your reply.
I run the command below.
docker run -v $PWD:/data --rm rkajitani/metaplatanus metaplatanus -IP1 /data/test.R1.fastq /data/test.R2.fastq -p /data/test.pac.fasta --o /data/out -t 50 -m 200 -tmp /data > log 2>&1
I got the out_contig.fa, but also I got the out.iteLog writing the error message below.
metaplatanus_core iterate -tmp /data -c initial_merged.fa initial_mergedJunctionKmer.fa -k /data/out_kmer_occ.bin -t 50 -m 200 -IP1 /data/test.R1.fastq /data/test.R2.fastq -p /data/test.pac.fasta -o /data/out
sh: 1: cannot create /data/out1//data/out_contig.fa: Directory nonexistent
Error(11): Error, Create link exception!!
ln, cp, mv or cat command failed.
Command exited with non-zero status 11
0.00user 0.00system 0:00.04elapsed 14%CPU (0avgtext+0avgdata 2052maxresident)k
201inputs+8outputs (1major+768minor)pagefaults 0swaps
Could you solve the problem?
Yuya
I notice that "/" in an argument of -o (--o) causes the error you reported. As a temporary solution, could you please try the command below?
docker run -v $PWD:/data --rm rkajitani/metaplatanus /bin/bash -c "cd /data && metaplatanus -IP1 /data/test.R1.fastq /data/test.R2.fastq -p /data/test.pac.fasta --o out -t 50 -m 200 -tmp /data > log 2>&1"
To resume your process (skip contig-assembly), please type the commands below.
mkdir -p out_intermediate/1_contig_asm
mv out_contig.fa out_intermediate/1_contig_asm/out_contig.fa
mv out_junctionKmer.fa out_intermediate/1_contig_asm/out_junctionKmer.fa
mv out_kmer_occ.bin out_intermediate/1_contig_asm/out_kmer_occ.bin
touch out_intermediate/1_contig_asm/done
MetaPlatanus detects a directory "out_intermediate/1_contig_asm" and its contens.
I'm sorry to bother you again.
Thanks for your reply. I could obtain results successfully.
Yuya
Thank you for informing! I will improve the usability...
Hi,
I use metaplatanus v1.3.0 by docker and got the same issue of https://github.com/rkajitani/MetaPlatanus/issues/1#issue-918384122
docker run -v $PWD:/data --rm rkajitani/metaplatanus metaplatanus -IP1 R1.fastq.gz R2.fastq.gz -p pacbio.fasta --o out -t 50 > log 2>&1
Could you solve the problem?
Yuya