Inappropriate ioctl for device on docker

[YuyaKiguchi]

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

[rkajitani]

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.

[Unaimend]

I had the same error with the conda installation. Which is metaplatanus v1.3.0

[YuyaKiguchi]

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

[rkajitani]

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.

[YuyaKiguchi]

Thanks for your reply. I could obtain results successfully.

Yuya

[rkajitani]

Thank you for informing! I will improve the usability...