[2023-06-05 01:08:34,260] [INFO] DFAST_QC pipeline started.
[2023-06-05 01:08:34,263] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 01:08:34,263] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference
[2023-06-05 01:08:35,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 01:08:35,596] [INFO] Task started: Prodigal
[2023-06-05 01:08:35,596] [INFO] Running command: gunzip -c /var/lib/cwl/stgc28c2bae-6776-4f8f-a2d4-822de30ddfc8/GCA_934593255.1_ERR7745403_bin.153_genomic.fna.gz | prodigal -d GCA_934593255.1_ERR7745403_bin.153_genomic.fna/cds.fna -a GCA_934593255.1_ERR7745403_bin.153_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 01:08:40,145] [INFO] Task succeeded: Prodigal
[2023-06-05 01:08:40,145] [INFO] Task started: HMMsearch
[2023-06-05 01:08:40,146] [INFO] Running command: hmmsearch --tblout GCA_934593255.1_ERR7745403_bin.153_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference/reference_markers.hmm GCA_934593255.1_ERR7745403_bin.153_genomic.fna/protein.faa > /dev/null
[2023-06-05 01:08:40,400] [INFO] Task succeeded: HMMsearch
[2023-06-05 01:08:40,401] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc28c2bae-6776-4f8f-a2d4-822de30ddfc8/GCA_934593255.1_ERR7745403_bin.153_genomic.fna.gz]
[2023-06-05 01:08:40,434] [INFO] Query marker FASTA was written to GCA_934593255.1_ERR7745403_bin.153_genomic.fna/markers.fasta
[2023-06-05 01:08:40,434] [INFO] Task started: Blastn
[2023-06-05 01:08:40,434] [INFO] Running command: blastn -query GCA_934593255.1_ERR7745403_bin.153_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference/reference_markers.fasta -out GCA_934593255.1_ERR7745403_bin.153_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:08:41,069] [INFO] Task succeeded: Blastn
[2023-06-05 01:08:41,073] [INFO] Selected 24 target genomes.
[2023-06-05 01:08:41,073] [INFO] Target genome list was writen to GCA_934593255.1_ERR7745403_bin.153_genomic.fna/target_genomes.txt
[2023-06-05 01:08:41,077] [INFO] Task started: fastANI
[2023-06-05 01:08:41,077] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28c2bae-6776-4f8f-a2d4-822de30ddfc8/GCA_934593255.1_ERR7745403_bin.153_genomic.fna.gz --refList GCA_934593255.1_ERR7745403_bin.153_genomic.fna/target_genomes.txt --output GCA_934593255.1_ERR7745403_bin.153_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 01:08:54,363] [INFO] Task succeeded: fastANI
[2023-06-05 01:08:54,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 01:08:54,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 01:08:54,370] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 01:08:54,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 01:08:54,371] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.7515	53	524	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 01:08:54,373] [INFO] DFAST Taxonomy check result was written to GCA_934593255.1_ERR7745403_bin.153_genomic.fna/tc_result.tsv
[2023-06-05 01:08:54,375] [INFO] ===== Taxonomy check completed =====
[2023-06-05 01:08:54,375] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 01:08:54,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference/checkm_data
[2023-06-05 01:08:54,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 01:08:54,399] [INFO] Task started: CheckM
[2023-06-05 01:08:54,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934593255.1_ERR7745403_bin.153_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934593255.1_ERR7745403_bin.153_genomic.fna/checkm_input GCA_934593255.1_ERR7745403_bin.153_genomic.fna/checkm_result
[2023-06-05 01:09:14,924] [INFO] Task succeeded: CheckM
[2023-06-05 01:09:14,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 01:09:14,944] [INFO] ===== Completeness check finished =====
[2023-06-05 01:09:14,944] [INFO] ===== Start GTDB Search =====
[2023-06-05 01:09:14,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934593255.1_ERR7745403_bin.153_genomic.fna/markers.fasta)
[2023-06-05 01:09:14,945] [INFO] Task started: Blastn
[2023-06-05 01:09:14,945] [INFO] Running command: blastn -query GCA_934593255.1_ERR7745403_bin.153_genomic.fna/markers.fasta -db /var/lib/cwl/stg98f7f1dc-8ec1-4ca9-92d6-edfc2ac88def/dqc_reference/reference_markers_gtdb.fasta -out GCA_934593255.1_ERR7745403_bin.153_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 01:09:15,877] [INFO] Task succeeded: Blastn
[2023-06-05 01:09:15,882] [INFO] Selected 16 target genomes.
[2023-06-05 01:09:15,883] [INFO] Target genome list was writen to GCA_934593255.1_ERR7745403_bin.153_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 01:09:15,893] [INFO] Task started: fastANI
[2023-06-05 01:09:15,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28c2bae-6776-4f8f-a2d4-822de30ddfc8/GCA_934593255.1_ERR7745403_bin.153_genomic.fna.gz --refList GCA_934593255.1_ERR7745403_bin.153_genomic.fna/target_genomes_gtdb.txt --output GCA_934593255.1_ERR7745403_bin.153_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 01:09:22,558] [INFO] Task succeeded: fastANI
[2023-06-05 01:09:22,574] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 01:09:22,574] [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_900549645.1	s__Limivicinus sp900549645	98.0123	428	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.52	99.05	0.92	0.86	3	conclusive
GCA_900547315.1	s__Limivicinus sp900547315	93.6887	408	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_003150355.1	s__Limivicinus sp003150355	79.6567	200	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	96.94	0.74	0.68	6	-
GCA_900549865.1	s__Limivicinus sp900549865	79.632	218	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.13	98.09	0.79	0.79	3	-
GCA_900546515.1	s__Limivicinus sp900546515	79.3878	189	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.98	99.98	0.95	0.95	2	-
GCA_900319695.1	s__Limivicinus sp900319695	78.8009	150	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.29	96.47	0.86	0.81	8	-
GCA_900319465.1	s__Limivicinus sp900319465	78.7777	177	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.77	99.67	0.93	0.92	4	-
GCA_905233595.1	s__Limivicinus sp905233595	78.7602	126	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785905.1	s__Limivicinus sp902785905	78.7535	146	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430985.1	s__Limivicinus sp017430985	78.7073	151	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321275.1	s__Limivicinus sp900321275	78.6482	140	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.70	95.66	0.85	0.80	7	-
GCA_017477695.1	s__Limivicinus sp017477695	78.4616	121	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789745.1	s__Limivicinus sp902789745	78.3638	134	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450075.1	s__Limivicinus sp002450075	78.2005	135	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.03	97.77	0.79	0.75	6	-
GCA_902760845.1	s__CAG-103 sp902760845	77.1327	89	524	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 01:09:22,577] [INFO] GTDB search result was written to GCA_934593255.1_ERR7745403_bin.153_genomic.fna/result_gtdb.tsv
[2023-06-05 01:09:22,577] [INFO] ===== GTDB Search completed =====
[2023-06-05 01:09:22,580] [INFO] DFAST_QC result json was written to GCA_934593255.1_ERR7745403_bin.153_genomic.fna/dqc_result.json
[2023-06-05 01:09:22,581] [INFO] DFAST_QC completed!
[2023-06-05 01:09:22,581] [INFO] Total running time: 0h0m48s