Hi,
I am new to command line ...and a bit confused regarding this:
SalmonTE.py index [--ref_name=ref_name] (--input_fasta=fa_file) [--te_only]
what does --te_only mean ? Do I have to give the TE annotation file ? but in which format ?
kindly help.
I tried running:
./SalmonTE.py quant --reference=hs example/CTRL_1_R1.fastq example/CTRL_2_R1.fastq
2021-04-08 15:43:40,525 Starting quantification mode
2021-04-08 15:43:40,525 Collecting FASTQ files...
2021-04-08 15:43:40,526 The input dataset is considered as a single-end dataset.
2021-04-08 15:43:40,526 Collected 2 FASTQ files.
2021-04-08 15:43:40,526 Quantification has been finished.
2021-04-08 15:43:40,526 Running Salmon using Snakemake
Job counts:
count jobs
1 all
1 collect_abundance
1 collect_mappability
2 run_salmon_fq
5
2021-04-08 15:43:40,668 Job counts:
count jobs
1 all
1 collect_abundance
1 collect_mappability
2 run_salmon_fq
5
Job counts:
count jobs
1 collect_mappability
1
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem.
Job counts:
count jobs
1 collect_abundance
1
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem.
Hi, I am new to command line ...and a bit confused regarding this:
SalmonTE.py index [--ref_name=ref_name] (--input_fasta=fa_file) [--te_only]what does --te_only mean ? Do I have to give the TE annotation file ? but in which format ? kindly help. I tried running: ./SalmonTE.py quant --reference=hs example/CTRL_1_R1.fastq example/CTRL_2_R1.fastq 2021-04-08 15:43:40,525 Starting quantification mode 2021-04-08 15:43:40,525 Collecting FASTQ files... 2021-04-08 15:43:40,526 The input dataset is considered as a single-end dataset. 2021-04-08 15:43:40,526 Collected 2 FASTQ files. 2021-04-08 15:43:40,526 Quantification has been finished. 2021-04-08 15:43:40,526 Running Salmon using Snakemake Job counts: count jobs 1 all 1 collect_abundance 1 collect_mappability 2 run_salmon_fq 5 2021-04-08 15:43:40,668 Job counts: count jobs 1 all 1 collect_abundance 1 collect_mappability 2 run_salmon_fq 5 Job counts: count jobs 1 collect_mappability 1 Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem. Job counts: count jobs 1 collect_abundance 1 Failed to solve scheduling problem with ILP solver. Falling back to greedy solver. Run Snakemake with --verbose to see the full solver output for debugging the problem.