long_reads_citation.txt

[davidmadariaga]

Hi!!!, hope you are doing great!. The program it's giving me this error, do you know what could be the reason?? Im attaching a screenshot. Feel free, please, to ask me whatever you want.

(snakemake_meta) [mdavid@n003 metagenomics_snakemake]$ snakemake -s Snakefile_long_reads_full_workflow --cores all Building DAG of jobs... MissingInputException in rule citation in file /home/bioren/mdavid/metagenomics_snakemake/rules/long_reads/rule_citation_long.snake, line 2: Missing input files for rule citation: output: /home/bioren/mdavid/UA/FONDECYTKATTIA/microbiomeanalyst_final/A/pruebasnakemake/output/long_reads/long_read_res04-Jul-2024-18/long_reads_citation.txt wildcards: wd=/home/bioren/mdavid/UA/FONDECYTKATTIA/microbiomeanalyst_final/A/pruebasnakemake, rs=long_read_res04-Jul-2024-18 affected files: /home/bioren/mdavid/UA/FONDECYTKATTIA/microbiomeanalyst_final/A/pruebasnakemake/citations/long_reads_citation.txt

Greetings from Chile, South America!!

[pablorr24]

Hi David, Is there a file called long_reads_citation.txt in the citations folder? It should have been included when you installed the repository. The error is telling you that this file wasn't found.

Feel free to reach out for any other questions.

Note: edited to refer to the right file name (typo)

[davidmadariaga]

Thanks for answering!, there's not!

[davidmadariaga]

there are only these ones: fastqc_citation.txt long_reads_citation.txt nanoplot_citation.txt post_analysis_citation.txt short_reads_citation.txt

[davidmadariaga]

my bad, i did not see it, what could be happening then?

[pablorr24]

I mistyped the file name earlier, I meant long_reads_citation.txt, so that's not the problem.

I think I know now what's the issue. You should edit your config file (config_templates/config_long_reads_full_workflow.yaml) and in the working_directory parameter you should set it to your main Snakemake Metagenomics folder (where you're running the main command). I believe it's this: /home/bioren/mdavid/UA/FONDECYTKATTIA/microbiomeanalyst_final/A/pruebasnakemake

You should also set up the other parameters if you haven't done so.

Any questions you can reach me directly as well.

[davidmadariaga]

ok, thanks!! i'll try the suggestions, thanks thanks

[davidmadariaga]

hi again!, now it's giving me this, any ideas why? feel free to answer whenever you can, thanks in advance!!

(snakemake_meta) [mdavid@mapudungun-frontend metagenomics_snakemake]$ snakemake -s Snakefile_long_reads_full_workflow --cores all Building DAG of jobs... File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_config_04-Jul-2024-20.yaml contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/otu_table_G.csv contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_reads_citation.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_config_04-Jul-2024-20.yaml contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/otu_table_G.csv contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//citations/long_reads_citation.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_reads_citation.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. Using shell: /usr/bin/bash Provided cores: 2 Rules claiming more threads will be scaled down. Job stats: job count

---

all 1 citation 1 create_otu_table_long 1 generate_config_file 1 post_check_rule_long 1 total 5

Select jobs to execute...

[Thu Jul 4 20:53:26 2024] rule generate_config_file: output: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_config_04-Jul-2024-20.yaml jobid: 1 reason: Missing output files: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_config_04-Jul-2024-20.yaml wildcards: wd=/home/bioren/mdavid/metagenomics_snakemake/, rs=long_read_res04-Jul-2024-20, ts=04-Jul-2024-20 resources: tmpdir=/tmp

[Thu Jul 4 20:53:26 2024] rule post_check_rule_long: output: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt jobid: 2 reason: Missing output files: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt wildcards: wd=/home/bioren/mdavid/metagenomics_snakemake/, rs=long_read_res04-Jul-2024-20 resources: tmpdir=/tmp

Building DAG of jobs... File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_config_04-Jul-2024-20.yaml contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. Building DAG of jobs... File path /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt contains double '/'. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake. Using shell: /usr/bin/bash Provided cores: 2 Using shell: /usr/bin/bash Rules claiming more threads will be scaled down. Provided cores: 2 Select jobs to execute... Rules claiming more threads will be scaled down. Select jobs to execute... Generated config file: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_config_04-Jul-2024-20.yaml [Thu Jul 4 20:53:28 2024] Finished job 1. 1 of 5 steps (20%) done Select jobs to execute...

[Thu Jul 4 20:53:28 2024] rule citation: input: /home/bioren/mdavid/metagenomics_snakemake//citations/long_reads_citation.txt output: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_reads_citation.txt jobid: 4 reason: Missing output files: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/long_reads_citation.txt wildcards: wd=/home/bioren/mdavid/metagenomics_snakemake/, rs=long_read_res04-Jul-2024-20 resources: tmpdir=/tmp

[Thu Jul 4 20:53:28 2024] Finished job 2. 2 of 5 steps (40%) done Select jobs to execute...

[Thu Jul 4 20:53:28 2024] rule create_otu_table_long: input: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt output: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/otu_table_G.csv jobid: 3 reason: Missing output files: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/otu_table_G.csv; Input files updated by another job: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt wildcards: wd=/home/bioren/mdavid/metagenomics_snakemake/, rs=long_read_res04-Jul-2024-20, lv=G resources: tmpdir=/tmp

Creating OTU table [Thu Jul 4 20:53:28 2024] Finished job 4. 3 of 5 steps (60%) done Traceback (most recent call last): File "/home/bioren/mdavid/metagenomics_snakemake/scripts/kraken2OTU.py", line 117, in file_dict = read_in_files(args.reportpathsfile) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/bioren/mdavid/metagenomics_snakemake/scripts/kraken2OTU.py", line 64, in read_in_files raise AssertionError("No report files found in the provided file!") AssertionError: No report files found in the provided file! [Thu Jul 4 20:53:28 2024] Error in rule create_otu_table_long: jobid: 3 input: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt output: /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/otu_table_G.csv shell:

    echo "Creating OTU table"
    python3 scripts/kraken2OTU.py --reportpathsfile /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/kraken_report_paths.txt --level G --outputfolder /home/bioren/mdavid/metagenomics_snakemake//output/long_reads/long_read_res04-Jul-2024-20/

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

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-07-04T205320.478090.snakemake.log

[pablorr24]

Just remove the last '/' from your working directory path in the config file. But that's a good observation, I'll make some changes to make this clear. I think your analysis should work soon :)

[davidmadariaga]

Hi, i changed the / at the end but it seems that im getting the same error, this is what i got:

(snakemake_meta) [mdavid@n003 metagenomics_snakemake]$ snakemake -s Snakefile_long_reads_full_workflow --cores 20 Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Job stats: job count

---

all 1 create_otu_table_long 1 total 2

Select jobs to execute...

[Fri Jul 5 16:37:38 2024] rule create_otu_table_long: input: /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/kraken_report_paths.txt output: /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/otu_table_G.csv jobid: 3 reason: Missing output files: /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/otu_table_G.csv wildcards: wd=/home/bioren/mdavid/metagenomics_snakemake, rs=long_read_res05-Jul-2024-16, lv=G resources: tmpdir=/tmp

Creating OTU table Traceback (most recent call last): File "/home/bioren/mdavid/metagenomics_snakemake/scripts/kraken2OTU.py", line 117, in file_dict = read_in_files(args.reportpathsfile) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/bioren/mdavid/metagenomics_snakemake/scripts/kraken2OTU.py", line 64, in read_in_files raise AssertionError("No report files found in the provided file!") AssertionError: No report files found in the provided file! [Fri Jul 5 16:37:38 2024] Error in rule create_otu_table_long: jobid: 3 input: /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/kraken_report_paths.txt output: /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/otu_table_G.csv shell:

    echo "Creating OTU table"
    python3 scripts/kraken2OTU.py --reportpathsfile /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/kraken_report_paths.txt --level G --outputfolder /home/bioren/mdavid/metagenomics_snakemake/output/long_reads/long_read_res05-Jul-2024-16/

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

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-07-05T163736.845480.snakemake.log

btw, this is my config file: (snakemake_meta) [mdavid@n003 config_templates]$ cat config_long_reads_full_workflow.yaml

Run the long-reads full workflow by configuring these file and typing in the terminal

snakemake -s Snakefile_long_reads_full_workflow --cores all

working_directory: /home/bioren/mdavid/metagenomics_snakemake

sample_path: /home/bioren/mdavid/UA/FONDECYTKATTIA/microbiomeanalyst_final/A/pruebasnakemake

database_path: /home/bioren/mdavid/centrifuge_last/centrifuge prefix: silva_16S_index

nanofilt_parameters: LENGTH: 1000 #default=0 QUALITY: 10 #default=0

Optional Parameteres

MAXLENGTH: 1900 MINGC: 0 MAXGC: 1 HEADCROP: 0 TAILCROP: 0

Centrifuge

centrifuge_parameters: max_hits: 5 #default=5

Diversity

alpha_diversity: "all" #options: all, Shannon, Simpson, Fischer, BP (Berger-Parkers)

Taxonomic Level

otu_table_level: G

thanks in advance, feel free to answer whenever you can.

Greetings!