Victoria Cepeda comments

Results 15 comments of


                                            Victoria Cepeda

snakemake: error: argument -T/--restart-times: expected one argument

did you run the Readme examples without errors? which command and samples did you run?

Error --pilon polish contigs

check your java installation. I didn't include it in the requirements but is needed by pilon

Error when running MetaCompass

Did you try the readme examples first? Also, please check if mc.sam and mc.sam.all are empty or have very few lines.

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

Hi, can you check if the assembly/contigs.fasta, assembly/megahit/final.contig.fa, or metacompass_output/metacompass.final.ctg.fa files are empy? Also, can you share the last log file in the log folder?

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

Can you post the command you ran? and also did you run the tutorial successfully?

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

Please check if your bowtie2 version is (>=) 2.2.9 and share the file example1_output/logs/bowtie2map.log

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

Bowtie2 is not working, can you run ls -lrt example1_output/assembly and share the output?

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

Do you get any output? can you ls all the folders from example1_output? You should get some output when running "bowtie2-build -o 3 --threads 4 -q Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/assembly/mc.index 1>> example1_output/assembly/mc.index...

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

Is seems like there is an issue with Bowtie2, not the metacompass installation. Can you run "bowtie2-build -o 3 --threads 4 -q Candidatus_Carsonella_ruddii_HT_Thao2000.fasta mc.index"

one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode

All scripts were written for python3. It seems like you have python 2 and 3 installed, and your pythonpath is pointed at python 2. Please ask your HPC expert how...