marco91sol

Error in funannotate predict pipeline

2

**Are you using the latest release?** I am using 1.8.10 version through docker nextgenusfs/funannotate container **Describe the bug** I am running funannotate predict on a de novo genome assembly of...

Masurca issue mega-reads pass 1 failed

3

Dear all, I am using Masurca for hybrid genome assembly through its conda version. I ran masurca config.txt and I received the following error (image attached)  How I could...

nextPolish on Docker

1

**Describe the bug** Hi, I ran nextPolish on docker. Firstly, I used the docker pull pvstodghill/nextpolish. Later, I ran the following command: docker run --ulimit nofile=64000:64000 -u $(id -u) -v...

NextPolish Installation

1

**Describe the bug** Compilation terminated with some errors **Error message** gcc -g -Wall -O2 -I. -I../../lib/htslib/ -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c bam_tview_curses.c:41:20: fatal error: curses.h: No such file or directory...

No TPM values, no reads processed

9

Hi, I am using TPMCalculator using the following command: TPMCalculator -g file.gtf -d ./ -a -p -e In the current directory, I have sorted bam files deriving from HISAT2 alignment...

Remove redundancy in braker.gtf

1

Hi, I launch BRAKER. Giving BUSCO analysis on the proteins deriving from braker.gtf , I noticed a strong duplication even due to redundancy. How can I remove it? An example...

The file ./braker/errors/optimize_augustus.stderr gives me the following output: How can I solve that? Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory /tmp/LEq6SDRWTp: No space left on device at /mnt/DATA/home/marcos/anaconda3/envs/maker/lib/site_perl/5.26.2/Parallel/ForkManager.pm...

BRAKER.gtf to EVM

1

Hi, Im trying to use Evidence Modeler on braker.gtf but with no result. I used both scripts for modifying it: 1. gtf2gff.pl 2. add_name_to_gff3.pl But, when I launch the validator...

MITObim usage

1

I launch the following command: ./MITObim.pl -end 10 -quick ~/COI_sequence.fasta -sample CS_test -ref reference-mt -readpool ~/CS/Illumina_reads/CS.fastq &>log It gives me as output the following: Can't exec "mirabait": No such file...

Dear all, I am running the following command for merging assemblies: `php ./MAC.php ~/assembly_1 ~/assembly_2 ~/IlluminaSRs_paired1.fastq ~/IlluminaSRs_paired2.fastq ~/MAC_output/` ERROR: Could not parse delta file, ~/MAC_output//Mix2.delta error no: 400 ERROR: Could...