[2024-01-25 19:42:50,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:50,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:50,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference
[2024-01-25 19:42:51,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:51,770] [INFO] Task started: Prodigal
[2024-01-25 19:42:51,770] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa532b2a-5c3f-414d-a5e2-de5a01934359/GCF_001688845.2_ASM168884v2_genomic.fna.gz | prodigal -d GCF_001688845.2_ASM168884v2_genomic.fna/cds.fna -a GCF_001688845.2_ASM168884v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:07,515] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:07,515] [INFO] Task started: HMMsearch
[2024-01-25 19:43:07,515] [INFO] Running command: hmmsearch --tblout GCF_001688845.2_ASM168884v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference/reference_markers.hmm GCF_001688845.2_ASM168884v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:07,743] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:07,744] [INFO] Found 6/6 markers.
[2024-01-25 19:43:07,770] [INFO] Query marker FASTA was written to GCF_001688845.2_ASM168884v2_genomic.fna/markers.fasta
[2024-01-25 19:43:07,771] [INFO] Task started: Blastn
[2024-01-25 19:43:07,771] [INFO] Running command: blastn -query GCF_001688845.2_ASM168884v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference/reference_markers.fasta -out GCF_001688845.2_ASM168884v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:08,311] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:08,313] [INFO] Selected 9 target genomes.
[2024-01-25 19:43:08,313] [INFO] Target genome list was writen to GCF_001688845.2_ASM168884v2_genomic.fna/target_genomes.txt
[2024-01-25 19:43:08,320] [INFO] Task started: fastANI
[2024-01-25 19:43:08,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa532b2a-5c3f-414d-a5e2-de5a01934359/GCF_001688845.2_ASM168884v2_genomic.fna.gz --refList GCF_001688845.2_ASM168884v2_genomic.fna/target_genomes.txt --output GCF_001688845.2_ASM168884v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:16,502] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:16,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:16,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:16,509] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:43:16,509] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:16,510] [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
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	100.0	1102	1102	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	99.996	1098	1102	95	conclusive
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	99.9955	1098	1102	95	conclusive
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	82.8426	144	1102	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	82.2871	146	1102	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	80.4848	216	1102	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	79.1628	137	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:16,511] [INFO] DFAST Taxonomy check result was written to GCF_001688845.2_ASM168884v2_genomic.fna/tc_result.tsv
[2024-01-25 19:43:16,511] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:16,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:16,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference/checkm_data
[2024-01-25 19:43:16,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:16,551] [INFO] Task started: CheckM
[2024-01-25 19:43:16,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001688845.2_ASM168884v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001688845.2_ASM168884v2_genomic.fna/checkm_input GCF_001688845.2_ASM168884v2_genomic.fna/checkm_result
[2024-01-25 19:44:02,353] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:02,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:02,378] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:02,378] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:02,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001688845.2_ASM168884v2_genomic.fna/markers.fasta)
[2024-01-25 19:44:02,380] [INFO] Task started: Blastn
[2024-01-25 19:44:02,380] [INFO] Running command: blastn -query GCF_001688845.2_ASM168884v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c2a260-a1d4-4b11-a095-ebff38dc301b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001688845.2_ASM168884v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:03,226] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:03,229] [INFO] Selected 23 target genomes.
[2024-01-25 19:44:03,229] [INFO] Target genome list was writen to GCF_001688845.2_ASM168884v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:03,274] [INFO] Task started: fastANI
[2024-01-25 19:44:03,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa532b2a-5c3f-414d-a5e2-de5a01934359/GCF_001688845.2_ASM168884v2_genomic.fna.gz --refList GCF_001688845.2_ASM168884v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001688845.2_ASM168884v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:18,759] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:18,772] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:18,773] [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_002201515.1	s__Muribaculum intestinale	99.9959	1097	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.09	97.90	0.92	0.80	20	conclusive
GCF_004803915.1	s__Duncaniella dubosii	82.2366	145	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	98.46	96.11	0.91	0.80	8	-
GCF_004803695.1	s__Muribaculum gordoncarteri	80.2864	213	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCA_004102785.1	s__UBA7173 sp002491305	80.2418	156	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.18	98.68	0.94	0.92	6	-
GCA_910583865.1	s__Muribaculum sp910583865	79.7529	423	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004102805.1	s__UBA7173 sp004102805	79.6218	141	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	98.86	98.86	0.92	0.89	3	-
GCA_910578835.1	s__Muribaculum sp910578835	78.1	174	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584825.1	s__Duncaniella sp910584825	77.9084	130	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Duncaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775605.1	s__Paramuribaculum sp009775605	77.7935	108	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	99.73	99.73	0.91	0.91	2	-
GCA_003150235.1	s__Muribaculum sp003150235	77.7074	156	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	-
GCA_905210435.1	s__UBA7173 sp905210435	77.5593	129	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001915385.1	s__UBA7173 sp001915385	77.5494	127	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.67	96.43	0.78	0.73	4	-
GCA_001689445.1	s__M3 sp001689445	77.5457	130	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__M3	95.0	99.97	99.97	0.98	0.98	2	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	77.5418	157	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_905193485.1	s__Paramuribaculum sp905193485	77.5353	80	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775095.1	s__Muribaculum sp009775095	77.5146	151	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCA_014801485.1	s__CAG-873 sp014801485	77.4435	81	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587665.1	s__Muribaculum sp910587665	77.3747	149	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578785.1	s__Muribaculum sp910578785	77.283	158	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586995.1	s__CAG-873 sp910586995	77.1488	82	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009177195.1	s__Muribaculum sp009177195	77.1167	92	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541865.1	s__CAG-873 sp900541865	77.0842	82	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587075.1	s__UBA7173 sp910587075	76.9231	103	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:18,782] [INFO] GTDB search result was written to GCF_001688845.2_ASM168884v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:18,783] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:18,788] [INFO] DFAST_QC result json was written to GCF_001688845.2_ASM168884v2_genomic.fna/dqc_result.json
[2024-01-25 19:44:18,789] [INFO] DFAST_QC completed!
[2024-01-25 19:44:18,789] [INFO] Total running time: 0h1m28s