[2023-06-05 18:09:35,616] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:09:35,618] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:09:35,618] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference
[2023-06-05 18:09:36,737] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:09:36,737] [INFO] Task started: Prodigal
[2023-06-05 18:09:36,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a6f4fac-60cc-4a4c-b213-f80ccb6c98b5/GCA_934351925.1_ERR7745362_bin.13_genomic.fna.gz | prodigal -d GCA_934351925.1_ERR7745362_bin.13_genomic.fna/cds.fna -a GCA_934351925.1_ERR7745362_bin.13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:09:43,596] [INFO] Task succeeded: Prodigal
[2023-06-05 18:09:43,597] [INFO] Task started: HMMsearch
[2023-06-05 18:09:43,597] [INFO] Running command: hmmsearch --tblout GCA_934351925.1_ERR7745362_bin.13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference/reference_markers.hmm GCA_934351925.1_ERR7745362_bin.13_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:09:43,806] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:09:43,808] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a6f4fac-60cc-4a4c-b213-f80ccb6c98b5/GCA_934351925.1_ERR7745362_bin.13_genomic.fna.gz]
[2023-06-05 18:09:43,833] [INFO] Query marker FASTA was written to GCA_934351925.1_ERR7745362_bin.13_genomic.fna/markers.fasta
[2023-06-05 18:09:43,834] [INFO] Task started: Blastn
[2023-06-05 18:09:43,834] [INFO] Running command: blastn -query GCA_934351925.1_ERR7745362_bin.13_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference/reference_markers.fasta -out GCA_934351925.1_ERR7745362_bin.13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:09:44,357] [INFO] Task succeeded: Blastn
[2023-06-05 18:09:44,360] [INFO] Selected 20 target genomes.
[2023-06-05 18:09:44,360] [INFO] Target genome list was writen to GCA_934351925.1_ERR7745362_bin.13_genomic.fna/target_genomes.txt
[2023-06-05 18:09:44,362] [INFO] Task started: fastANI
[2023-06-05 18:09:44,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6f4fac-60cc-4a4c-b213-f80ccb6c98b5/GCA_934351925.1_ERR7745362_bin.13_genomic.fna.gz --refList GCA_934351925.1_ERR7745362_bin.13_genomic.fna/target_genomes.txt --output GCA_934351925.1_ERR7745362_bin.13_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:09:57,111] [INFO] Task succeeded: fastANI
[2023-06-05 18:09:57,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:09:57,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:09:57,115] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:09:57,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:09:57,115] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	77.5279	54	988	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:09:57,128] [INFO] DFAST Taxonomy check result was written to GCA_934351925.1_ERR7745362_bin.13_genomic.fna/tc_result.tsv
[2023-06-05 18:09:57,129] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:09:57,129] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:09:57,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference/checkm_data
[2023-06-05 18:09:57,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:09:57,165] [INFO] Task started: CheckM
[2023-06-05 18:09:57,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934351925.1_ERR7745362_bin.13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934351925.1_ERR7745362_bin.13_genomic.fna/checkm_input GCA_934351925.1_ERR7745362_bin.13_genomic.fna/checkm_result
[2023-06-05 18:10:22,519] [INFO] Task succeeded: CheckM
[2023-06-05 18:10:22,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:10:22,538] [INFO] ===== Completeness check finished =====
[2023-06-05 18:10:22,539] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:10:22,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934351925.1_ERR7745362_bin.13_genomic.fna/markers.fasta)
[2023-06-05 18:10:22,540] [INFO] Task started: Blastn
[2023-06-05 18:10:22,540] [INFO] Running command: blastn -query GCA_934351925.1_ERR7745362_bin.13_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5df467a-839e-420c-ba1f-a1b74e6cfb17/dqc_reference/reference_markers_gtdb.fasta -out GCA_934351925.1_ERR7745362_bin.13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:10:23,603] [INFO] Task succeeded: Blastn
[2023-06-05 18:10:23,606] [INFO] Selected 13 target genomes.
[2023-06-05 18:10:23,606] [INFO] Target genome list was writen to GCA_934351925.1_ERR7745362_bin.13_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:10:23,622] [INFO] Task started: fastANI
[2023-06-05 18:10:23,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6f4fac-60cc-4a4c-b213-f80ccb6c98b5/GCA_934351925.1_ERR7745362_bin.13_genomic.fna.gz --refList GCA_934351925.1_ERR7745362_bin.13_genomic.fna/target_genomes_gtdb.txt --output GCA_934351925.1_ERR7745362_bin.13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:10:31,079] [INFO] Task succeeded: fastANI
[2023-06-05 18:10:31,084] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:10:31,085] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_003486385.1	s__CAG-882 sp003486385	86.1109	620	988	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	98.36	97.90	0.89	0.87	6	-
GCA_900545175.1	s__CAG-882 sp900545175	83.4441	595	988	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	99.03	98.05	0.94	0.87	3	-
GCA_000435595.1	s__CAG-882 sp000435595	82.6274	552	988	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	98.75	98.61	0.86	0.85	4	-
GCA_900545455.1	s__CAG-882 sp900545455	81.9912	476	988	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431815.1	s__Butyrivibrio_A sp000431815	77.1945	63	988	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.85	98.85	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-05 18:10:31,086] [INFO] GTDB search result was written to GCA_934351925.1_ERR7745362_bin.13_genomic.fna/result_gtdb.tsv
[2023-06-05 18:10:31,087] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:10:31,089] [INFO] DFAST_QC result json was written to GCA_934351925.1_ERR7745362_bin.13_genomic.fna/dqc_result.json
[2023-06-05 18:10:31,089] [INFO] DFAST_QC completed!
[2023-06-05 18:10:31,089] [INFO] Total running time: 0h0m55s