[2024-01-24 13:13:46,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:46,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:46,723] [INFO] DQC Reference Directory: /var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference
[2024-01-24 13:13:48,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:48,006] [INFO] Task started: Prodigal
[2024-01-24 13:13:48,006] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a4d2503-cd23-4751-a518-d3d1d468da7a/GCF_009754915.1_ASM975491v1_genomic.fna.gz | prodigal -d GCF_009754915.1_ASM975491v1_genomic.fna/cds.fna -a GCF_009754915.1_ASM975491v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:03,904] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:03,904] [INFO] Task started: HMMsearch
[2024-01-24 13:14:03,904] [INFO] Running command: hmmsearch --tblout GCF_009754915.1_ASM975491v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference/reference_markers.hmm GCF_009754915.1_ASM975491v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:04,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:04,220] [INFO] Found 6/6 markers.
[2024-01-24 13:14:04,259] [INFO] Query marker FASTA was written to GCF_009754915.1_ASM975491v1_genomic.fna/markers.fasta
[2024-01-24 13:14:04,260] [INFO] Task started: Blastn
[2024-01-24 13:14:04,260] [INFO] Running command: blastn -query GCF_009754915.1_ASM975491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference/reference_markers.fasta -out GCF_009754915.1_ASM975491v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:04,865] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:04,869] [INFO] Selected 26 target genomes.
[2024-01-24 13:14:04,870] [INFO] Target genome list was writen to GCF_009754915.1_ASM975491v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:04,894] [INFO] Task started: fastANI
[2024-01-24 13:14:04,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a4d2503-cd23-4751-a518-d3d1d468da7a/GCF_009754915.1_ASM975491v1_genomic.fna.gz --refList GCF_009754915.1_ASM975491v1_genomic.fna/target_genomes.txt --output GCF_009754915.1_ASM975491v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:26,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:26,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:26,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:26,909] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:26,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:26,909] [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
Mucilaginibacter arboris	strain=HMF7410	GCA_009754915.1	2682090	2682090	type	True	100.0	1352	1354	95	conclusive
Mucilaginibacter humi	strain=S1162	GCA_013087555.1	2732510	2732510	type	True	77.167	63	1354	95	below_threshold
Mucilaginibacter gracilis	strain=DSM 18602	GCA_003633615.1	423350	423350	type	True	76.8441	142	1354	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	76.8212	109	1354	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	76.7077	128	1354	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	76.6778	130	1354	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	76.6349	131	1354	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	76.5949	83	1354	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	76.5897	85	1354	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	76.5269	64	1354	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.5026	88	1354	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	76.4977	150	1354	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	76.4901	143	1354	95	below_threshold
Pedobacter puniceum	strain=HX-22-1	GCA_009674685.1	2666136	2666136	type	True	76.4763	89	1354	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.4533	98	1354	95	below_threshold
Mucilaginibacter paludis	strain=DSM 18603	GCA_000166195.3	423351	423351	type	True	76.4255	161	1354	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	76.424	129	1354	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	76.4149	132	1354	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	76.4147	137	1354	95	below_threshold
Pedobacter changchengzhani	strain=E01020	GCA_004354365.1	2529274	2529274	type	True	76.3446	65	1354	95	below_threshold
Pedobacter glucosidilyticus	strain=DSM 23534	GCA_000425145.1	1122941	1122941	type	True	76.2706	78	1354	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	75.9666	89	1354	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	75.9588	91	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:26,911] [INFO] DFAST Taxonomy check result was written to GCF_009754915.1_ASM975491v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:26,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:26,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:26,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference/checkm_data
[2024-01-24 13:14:26,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:26,956] [INFO] Task started: CheckM
[2024-01-24 13:14:26,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009754915.1_ASM975491v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009754915.1_ASM975491v1_genomic.fna/checkm_input GCF_009754915.1_ASM975491v1_genomic.fna/checkm_result
[2024-01-24 13:15:12,814] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:12,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:12,833] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:12,834] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:12,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009754915.1_ASM975491v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:12,834] [INFO] Task started: Blastn
[2024-01-24 13:15:12,835] [INFO] Running command: blastn -query GCF_009754915.1_ASM975491v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8ac2614-19c2-4f74-afb3-be64a9230f93/dqc_reference/reference_markers_gtdb.fasta -out GCF_009754915.1_ASM975491v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:13,660] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:13,664] [INFO] Selected 19 target genomes.
[2024-01-24 13:15:13,664] [INFO] Target genome list was writen to GCF_009754915.1_ASM975491v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:13,685] [INFO] Task started: fastANI
[2024-01-24 13:15:13,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a4d2503-cd23-4751-a518-d3d1d468da7a/GCF_009754915.1_ASM975491v1_genomic.fna.gz --refList GCF_009754915.1_ASM975491v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009754915.1_ASM975491v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:28,359] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:28,378] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:28,379] [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
GCF_009754915.1	s__Mucilaginibacter_A arboris	100.0	1352	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903642215.1	s__Mucilaginibacter_A sp903642215	80.2993	687	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288485.1	s__Mucilaginibacter sp013288485	77.0834	62	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013287375.1	s__Mucilaginibacter sp013287375	77.0221	67	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.48	99.44	0.60	0.60	3	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	76.9272	105	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_003633615.1	s__Mucilaginibacter gracilis	76.8441	142	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	76.6861	110	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288235.1	s__Mucilaginibacter sp013288235	76.6814	87	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	76.6533	115	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	76.5112	96	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	76.511	150	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898335.1	s__Mucilaginibacter sp001898335	76.4394	95	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.32	99.30	0.92	0.89	3	-
GCF_900100945.1	s__Mucilaginibacter gossypii	76.4149	132	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_014643835.1	s__Mucilaginibacter rubeus	76.4147	137	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	76.3235	99	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	76.2928	113	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCA_018267005.1	s__Mucilaginibacter sp018267005	76.1554	52	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286325.1	s__Mucilaginibacter sp013286325	76.1154	69	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885865.1	s__Mucilaginibacter sp903885865	75.7047	75	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.00	99.00	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:28,382] [INFO] GTDB search result was written to GCF_009754915.1_ASM975491v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:28,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:28,386] [INFO] DFAST_QC result json was written to GCF_009754915.1_ASM975491v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:28,386] [INFO] DFAST_QC completed!
[2024-01-24 13:15:28,387] [INFO] Total running time: 0h1m42s