mindinhead
commented
4 years ago I think you need to use the FASTA format as the input of your Nanopore data, instead of FASTQ (/home/puratos-l1/Assemblies/SunUP/P2707_Masurca_Hybrid/P2707_Raw_Guppy_output_porechop_trimmed_fastq_trimmed_1kb_Q7_reads.fastq).
Hi,
I'm trying to run masurca with a hybrid assembly of illumina PE and Nanopore data and I get the following error after running the config file:
Error line 23 of configuration file 'sr_config_SunUP_Hybrid.txt': invalid file for NANOPORE: '/home/puratos-l1/Assemblies/SunUP/P2707_Masurca_Hybrid/P2707_Raw_Guppy_output_porechop_trimmed_fastq_trimmed_1kb_Q7_reads.fastq' Bad file descriptor
I've checked the config file and as indicated I have the full path to the Nanopore reads: DATA
Illumina paired end reads supplied as
if single-end, do not specify
MUST HAVE Illumina paired end reads to use MaSuRCA
PE= pe 150 20 /home/puratos-l1/Sequenced_Genomes_RawReads/SunUP/SunUP_1_FCHCL7TBBXY_L7_WGS190904001-PUR-41_1.fq /home/puratos-l1/Sequenced_Genomes_RawReads/SunUP/SunUP_1_FCHCL7TBBXY_L7_WGS190904001-PUR-41_2.fq
Illumina mate pair reads supplied as
JUMP= sh 3600 200 /FULL_PATH/short_1.fastq /FULL_PATH/short_2.fastq
pacbio OR nanopore reads must be in a single fasta or fastq file with absolute path, can be gzipped
if you have both types of reads supply them both as NANOPORE type
PACBIO=/FULL_PATH/pacbio.fa
NANOPORE=/home/puratos-l1/Assemblies/SunUP/P2707_Masurca_Hybrid/P2707_Raw_Guppy_output_porechop_trimmed_fastq_trimmed_1kb_Q7_reads.fastq
Other reads (Sanger, 454, etc) one frg file, concatenate your frg files into one if you have many
OTHER=/FULL_PATH/file.frg
synteny-assisted assembly, concatenate all reference genomes into one reference.fa; works for Illumina-only data
REFERENCE=/FULL_PATH/nanopore.fa
END
I've tried looking for a similar problem in the forum but could not find any thing.
If I run masurca with only Illumina reads it works perfect.
Any ideas?
Thanks