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bergmanlab / mcclintock

Meta-pipeline to identify transposable element insertions using next generation sequencing data
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Snakefile is not on where is not suppose to be #122

Open Tcvalenzuela opened 9 months ago

Tcvalenzuela commented 9 months ago

Hi,

Thank you so much for this metapipeliene seems to be very useful. Nonetheless I have problems to starts to test.

After installing I run the test but is asking me to have Snakefile in a place that is not. And to be honest I don't understand what is trying to copy. Can you help me?

mcclintock) tcarrasco@pbil-deb:/beegfs/data/tcarrasco/Programs/mcclintock/test$ python3 ../mcclintock.py -r sacCer2.fasta -c sac_cer_TE_seqs.fasta -g reference_TE_locations.gff -t sac_cer_te_families.tsv -1 SRR800842_1.fastq.gz -2 SRR800842_2.fastq.gz -p 4 -o .
SETUP            checking fasta: /beegfs/data/tcarrasco/Programs/mcclintock/test/sacCer2.fasta
SETUP            checking fastq: /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1.fastq.gz
SETUP            checking fastq: /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_2.fastq.gz
SETUP            checking fasta: /beegfs/data/tcarrasco/Programs/mcclintock/test/sac_cer_TE_seqs.fasta
SETUP            checking locations gff: /beegfs/data/tcarrasco/Programs/mcclintock/test/reference_TE_locations.gff
SETUP            checking taxonomy TSV: /beegfs/data/tcarrasco/Programs/mcclintock/test/sac_cer_te_families.tsv
SETUP            McClintock Version: 2a1bec1c15c15c0c72ef351c64cb2a8058375e5c
cp: cannot stat '/beegfs/data/tcarrasco/Programs/Snakefile': No such file or directory
cp /beegfs/data/tcarrasco/Programs/Snakefile /beegfs/data/tcarrasco/Programs/mcclintock/test/snakemake/2214550
Error: no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile.
snakemake --use-conda --conda-prefix /beegfs/data/tcarrasco/Programs/install/envs/conda --configfile /beegfs/data/tcarrasco/Programs/mcclintock/test/snakemake/config/config_2214550.json --cores 4 --quiet /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/ngs_te_mapper/SRR800842_1_ngs_te_mapper_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/ngs_te_mapper2/SRR800842_1_ngs_te_mapper2_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/relocate/SRR800842_1_relocate_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/relocate2/SRR800842_1_relocate2_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/temp/SRR800842_1_temp_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/temp2/SRR800842_1_temp2_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/retroseq/SRR800842_1_retroseq_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/popoolationte/SRR800842_1_popoolationte_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/popoolationte2/SRR800842_1_popoolationte2_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/te-locate/SRR800842_1_telocate_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/teflon/SRR800842_1_teflon_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/coverage/te_depth.csv /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/intermediate/fastq/SRR800842_1_1.fq /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/intermediate/mapped_reads/median_insert.size /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/tebreak/SRR800842_1_tebreak_nonredundant.bed /beegfs/data/tcarrasco/Programs/mcclintock/test/SRR800842_1/results/summary/data/run/summary_report.txt