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Badhan023 / HTARGfinder

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Error running HTARGfinder #6

Open senukobla opened 2 months ago

senukobla commented 2 months ago

Hi , We are interested in this pipeline and are attempting to use for our work . We get error belw when we run it. Any solutions you suggest ?

Finished parsing hits for 33 of 33 (100.00%) bins. [2024-08-30 19:22:04] INFO: QA information written to: BAP1100000_checkm.csv [2024-08-30 19:22:04] INFO: { Current stage: 0:00:06.971 || Total: 0:16:01.255 } checkm-genome done python3: can't open file 'filtering_bins.py': [Errno 2] No such file or directory filtering done bash: remove.sh: No such file or directory removing done bin.10.fa usage: gtdbtk classify_wf (--genome_dir GENOME_DIR | --batchfile BATCHFILE) --out_dir OUT_DIR (--skip_ani_screen | --mash_db MASH_DB) [--no_mash] [--mash_k MASH_K] [--mash_s MASH_S] [--mash_v MASH_V] [--mash_max_distance MASH_MAX_DISTANCE] [-f] [-x EXTENSION] [--min_perc_aa MIN_PERC_AA] [--prefix PREFIX] [--genes] [--cpus CPUS] [--pplacer_cpus PPLACER_CPUS] [--force] [--scratch_dir SCRATCH_DIR] [--write_single_copy_genes] [--keep_intermediates] [--min_af MIN_AF] [--tmpdir TMPDIR] [--debug] [-h] gtdbtk classify_wf: error: one of the arguments --skip_ani_screen --mash_db is required gtdb-tookit done makeblastdb,blastn not detected, program exited! blastn,mafft,blastp not detected, program exited! MetaCHIP done diamond v0.9.14.115 | by Benjamin Buchfink buchfink@gmail.com Licensed under the GNU AGPL https://www.gnu.org/licenses/agpl.txt Check http://github.com/bbuchfink/diamond for updates.

CPU threads: 28

Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)

Target sequences to report alignments for: 25

Temporary directory: Opening the database... No such file or directory [0.000283s] Error: Error opening file reference_DeepARG-DB.dmnd diamond v0.9.14.115 | by Benjamin Buchfink buchfink@gmail.com Licensed under the GNU AGPL https://www.gnu.org/licenses/agpl.txt Check http://github.com/bbuchfink/diamond for updates.

CPU threads: 28

Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)

Target sequences to report alignments for: 25

Temporary directory: Opening the database... No such file or directory [0.000219s] Error: Error opening file reference_CARD.dmnd DIAMOND done python3: can't open file 'cross_checking.py': [Errno 2] No such file or directory python3: can't open file 'cross_checking.py': [Errno 2] No such file or directory cross-checking done pipeline ends

A

Badhan023 commented 2 months ago

Hi! Have you been able to follow the step-by-step installation guide? You have to run setup.sh, or you can install all the packages mentioned in that file and run those separately in the terminal. Since it shows that filtering_bins.py and remove.sh files were not found, have you cloned the whole repository properly? Otherwise, if you run pipeline.sh, it should find those files because they are in the same directory. You must be in the same directory while running; otherwise, these error messages will appear. What is happening is that from the filtering step, it is not working because the pipeline is connected in that way. Also, since it is not finding packages like makeblastdb and blastn, I am guessing the setup is not done properly. I would suggest you delete your cloned folder and redo the same thing. Adequately do the setup first with the conda environment setting and make sure all the necessary packages are appropriately installed.