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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Error in workflow mapping #271

Open sallesmath opened 2 years ago

sallesmath commented 2 years ago

Hello!

This has been discussed previously and I've read those posts , but I'm still having the following error:

(phyluce-1.7.1) sallesmath@DESKTOP-NQCD32J:~/dados_uce/phyluce_dados_uce_tropidurus/mapping$ phyluce_workflow --config config.yaml --output results_mapping --workflow mapping --cores 4
[WARNING] Output directory exists, REMOVE [y/n]: y
Building DAG of jobs...
MissingInputException in line 39 of /home/sallesmath/anaconda3/envs/phyluce-1.7.1/phyluce/workflows/mapping/Snakefile:
Missing input files for rule copy_and_build_index:
/home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204349.contigs.fasta

This is my config.yaml file:

reads:
    amcc-204349: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-amcc/amcc-204349/
    amcc-204498: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-amcc/amcc-204498/
    amcc-204357: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-amcc/amcc-204357/
    amcc-204384: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-amcc/amcc-204384/
    amcc-204510: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-amcc/amcc-204510/
    chunb-74137: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74137/
    chunb-74145: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74145/
    chunb-74146: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74146/
    chunb-74147: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74147/
    chunb-74155: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74155/
    chunb-74156: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74156/
    chunb-74157: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74157/
    chunb-74163: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74163/
    chunb-74162: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-chunb/chunb-74162/
    lg-15512987: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-lg/lg-15512987/
    mtr-29592: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-mtr/mtr-29592/
    mtr-29503: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-mtr/mtr-29503/
    mtr-29622: /home/dados_uce/phyluce_dados_uce_tropidurus/raw-fastq/raw-fastq-mtr/mtr-29622/

contigs:
    amcc-204349: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204349.contigs.fasta
    amcc-204498: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204498.contigs.fasta
    amcc-204357: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204357.contigs.fasta
    amcc-204384: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204384.contigs.fasta
    amcc-204510: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204510.contigs.fasta
    chunb-74137: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74137.contigs.fasta
    chunb-74145: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74145.contigs.fasta
    chunb-74146: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74146.contigs.fasta
    chunb-74147: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74147.contigs.fasta
    chunb-74155: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74155.contigs.fasta
    chunb-74156: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74156.contigs.fasta
    chunb-74157: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74157.contigs.fasta
    chunb-74163: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74163.contigs.fasta
    chunb-74162: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/chunb-74162.contigs.fasta
    lg-15512987: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/lg-15512987.contigs.fasta
    mtr-29592: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/mtr-29592.contigs.fasta
    mtr-29503: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/mtr-29503.contigs.fasta
    mtr-29622: /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/mtr-29622.contigs.fasta

I've already tried checking the configuration file several times, renamed the sequence files, changed the configuration of r1 and r2_pattern, but nothing worked.

Do you have any idea as to what might be going on?

Thanks!

brantfaircloth commented 2 years ago

To make things easier, I would work with a small (1-2 sample) config file. Then, ensure the path to the file actually exists (e.g. is there really a file at /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204349.contigs.fasta)?

If there is something at the path, is it a symlink at /home/dados_uce/phyluce_dados_uce_tropidurus/spades-assemblies/contigs/amcc-204349.contigs.fasta or a real file? If a symlink, copy the file somewhere else (using cp - this should place a real file copy in the new location), then update the config file and try again.

sallesmath commented 2 years ago

Hello again Dr. Faircloth, thanks for your quick response!

I managed to solve the problem by removing all the hyphens and underscores from the configuration file, writing the sample and contig names in the same way (e.g. amcc204349 and not amcc-204349, or amcc_204349).

Again, thank you for your time.

Best regards, Matheus.