[2023-06-05 03:27:58,916] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:27:58,920] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:27:58,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference
[2023-06-05 03:28:00,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:28:00,651] [INFO] Task started: Prodigal
[2023-06-05 03:28:00,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a963c46-8482-4dc9-9e90-a5e87775c5d6/GCA_934591815.1_ERR7745625_bin.181_genomic.fna.gz | prodigal -d GCA_934591815.1_ERR7745625_bin.181_genomic.fna/cds.fna -a GCA_934591815.1_ERR7745625_bin.181_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:28:07,279] [INFO] Task succeeded: Prodigal
[2023-06-05 03:28:07,279] [INFO] Task started: HMMsearch
[2023-06-05 03:28:07,279] [INFO] Running command: hmmsearch --tblout GCA_934591815.1_ERR7745625_bin.181_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference/reference_markers.hmm GCA_934591815.1_ERR7745625_bin.181_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:28:07,530] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:28:07,531] [INFO] Found 6/6 markers.
[2023-06-05 03:28:07,553] [INFO] Query marker FASTA was written to GCA_934591815.1_ERR7745625_bin.181_genomic.fna/markers.fasta
[2023-06-05 03:28:07,554] [INFO] Task started: Blastn
[2023-06-05 03:28:07,554] [INFO] Running command: blastn -query GCA_934591815.1_ERR7745625_bin.181_genomic.fna/markers.fasta -db /var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference/reference_markers.fasta -out GCA_934591815.1_ERR7745625_bin.181_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:08,344] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:08,348] [INFO] Selected 14 target genomes.
[2023-06-05 03:28:08,348] [INFO] Target genome list was writen to GCA_934591815.1_ERR7745625_bin.181_genomic.fna/target_genomes.txt
[2023-06-05 03:28:08,352] [INFO] Task started: fastANI
[2023-06-05 03:28:08,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a963c46-8482-4dc9-9e90-a5e87775c5d6/GCA_934591815.1_ERR7745625_bin.181_genomic.fna.gz --refList GCA_934591815.1_ERR7745625_bin.181_genomic.fna/target_genomes.txt --output GCA_934591815.1_ERR7745625_bin.181_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:28:15,539] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:15,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:28:15,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:28:15,552] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:28:15,552] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:28:15,552] [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	81.7247	330	716	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	81.0298	252	716	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.8955	213	716	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.2499	180	716	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.0731	142	716	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.0282	148	716	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.5542	115	716	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.3748	129	716	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.242	104	716	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	77.2264	68	716	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	77.1838	69	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:28:15,555] [INFO] DFAST Taxonomy check result was written to GCA_934591815.1_ERR7745625_bin.181_genomic.fna/tc_result.tsv
[2023-06-05 03:28:15,555] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:28:15,555] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:28:15,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference/checkm_data
[2023-06-05 03:28:15,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:28:15,583] [INFO] Task started: CheckM
[2023-06-05 03:28:15,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934591815.1_ERR7745625_bin.181_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934591815.1_ERR7745625_bin.181_genomic.fna/checkm_input GCA_934591815.1_ERR7745625_bin.181_genomic.fna/checkm_result
[2023-06-05 03:28:41,051] [INFO] Task succeeded: CheckM
[2023-06-05 03:28:41,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:28:41,074] [INFO] ===== Completeness check finished =====
[2023-06-05 03:28:41,075] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:28:41,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934591815.1_ERR7745625_bin.181_genomic.fna/markers.fasta)
[2023-06-05 03:28:41,076] [INFO] Task started: Blastn
[2023-06-05 03:28:41,076] [INFO] Running command: blastn -query GCA_934591815.1_ERR7745625_bin.181_genomic.fna/markers.fasta -db /var/lib/cwl/stg9021dc9d-6cf4-4010-b0af-d6834e39909e/dqc_reference/reference_markers_gtdb.fasta -out GCA_934591815.1_ERR7745625_bin.181_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:28:42,515] [INFO] Task succeeded: Blastn
[2023-06-05 03:28:42,519] [INFO] Selected 10 target genomes.
[2023-06-05 03:28:42,520] [INFO] Target genome list was writen to GCA_934591815.1_ERR7745625_bin.181_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:28:42,521] [INFO] Task started: fastANI
[2023-06-05 03:28:42,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a963c46-8482-4dc9-9e90-a5e87775c5d6/GCA_934591815.1_ERR7745625_bin.181_genomic.fna.gz --refList GCA_934591815.1_ERR7745625_bin.181_genomic.fna/target_genomes_gtdb.txt --output GCA_934591815.1_ERR7745625_bin.181_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:28:46,670] [INFO] Task succeeded: fastANI
[2023-06-05 03:28:46,683] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 03:28:46,683] [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_900545495.1	s__CAG-83 sp900545495	94.8759	502	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCA_900551355.1	s__CAG-83 sp900551355	89.7384	316	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.94	98.90	0.93	0.92	3	-
GCA_900547745.1	s__CAG-83 sp900547745	88.9315	419	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_900550585.1	s__CAG-83 sp900550585	88.7661	400	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.85	99.85	0.92	0.92	2	-
GCA_900545585.1	s__CAG-83 sp900545585	87.4299	450	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.41	98.11	0.88	0.81	5	-
GCA_003487665.1	s__CAG-83 sp003487665	84.8845	362	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.43	97.11	0.80	0.74	11	-
GCA_900551995.1	s__CAG-83 sp900551995	84.8545	377	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	97.61	0.85	0.83	3	-
GCA_900554275.1	s__CAG-83 sp900554275	84.0878	341	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.46	96.91	0.80	0.75	4	-
GCA_900556015.1	s__CAG-83 sp900556015	83.4378	219	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.42	97.27	0.78	0.77	3	-
GCA_000435555.1	s__CAG-83 sp000435555	83.083	317	716	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.91	97.56	0.88	0.73	17	-
--------------------------------------------------------------------------------
[2023-06-05 03:28:46,685] [INFO] GTDB search result was written to GCA_934591815.1_ERR7745625_bin.181_genomic.fna/result_gtdb.tsv
[2023-06-05 03:28:46,686] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:28:46,689] [INFO] DFAST_QC result json was written to GCA_934591815.1_ERR7745625_bin.181_genomic.fna/dqc_result.json
[2023-06-05 03:28:46,689] [INFO] DFAST_QC completed!
[2023-06-05 03:28:46,689] [INFO] Total running time: 0h0m48s