[2024-01-24 14:39:00,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:00,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:00,978] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference
[2024-01-24 14:39:02,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:02,325] [INFO] Task started: Prodigal
[2024-01-24 14:39:02,325] [INFO] Running command: gunzip -c /var/lib/cwl/stg23eb8fc0-66cd-478a-8c9c-367848805a48/GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/cds.fna -a GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:18,971] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:18,972] [INFO] Task started: HMMsearch
[2024-01-24 14:39:18,972] [INFO] Running command: hmmsearch --tblout GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference/reference_markers.hmm GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:19,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:19,292] [INFO] Found 6/6 markers.
[2024-01-24 14:39:19,326] [INFO] Query marker FASTA was written to GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:39:19,327] [INFO] Task started: Blastn
[2024-01-24 14:39:19,327] [INFO] Running command: blastn -query GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference/reference_markers.fasta -out GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:19,977] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:19,980] [INFO] Selected 23 target genomes.
[2024-01-24 14:39:19,981] [INFO] Target genome list was writen to GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:39:19,989] [INFO] Task started: fastANI
[2024-01-24 14:39:19,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg23eb8fc0-66cd-478a-8c9c-367848805a48/GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna.gz --refList GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:37,600] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:37,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:37,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:37,616] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:37,616] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:37,617] [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
Bacteroides luti	strain=DSM 26991	GCA_900128905.1	1297750	1297750	type	True	100.0	1353	1354	95	conclusive
Bacteroides finegoldii	strain=DSM 17565	GCA_000156195.1	338188	338188	suspected-type	True	77.7457	107	1354	95	below_threshold
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	77.6981	109	1354	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	77.6669	110	1354	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	77.6416	144	1354	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	77.5708	120	1354	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	77.5598	117	1354	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_000226135.2	674529	674529	type	True	77.541	128	1354	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	77.535	130	1354	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	77.4786	141	1354	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	77.4066	131	1354	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.3338	91	1354	95	below_threshold
Bacteroides coprosuis	strain=DSM 18011	GCA_000212915.1	151276	151276	type	True	77.2694	61	1354	95	below_threshold
Bacteroides ihuae	strain=Marseille-P2824	GCA_900104585.1	1852362	1852362	type	True	77.2453	151	1354	95	below_threshold
Bacteroides faecichinchillae	strain=JCM 17102	GCA_000614145.1	871325	871325	type	True	77.1681	138	1354	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	77.1488	139	1354	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	77.1447	85	1354	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	77.0946	97	1354	95	below_threshold
Bacteroides graminisolvens	strain=DSM 19988	GCA_000428125.1	477666	477666	type	True	76.9076	135	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:37,618] [INFO] DFAST Taxonomy check result was written to GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:39:37,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:37,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:37,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference/checkm_data
[2024-01-24 14:39:37,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:37,663] [INFO] Task started: CheckM
[2024-01-24 14:39:37,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/checkm_input GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:40:27,019] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:27,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:27,049] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:27,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:27,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:40:27,050] [INFO] Task started: Blastn
[2024-01-24 14:40:27,050] [INFO] Running command: blastn -query GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca28644-bc16-42d3-9f91-18084aa83f4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:27,980] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:27,983] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:27,983] [INFO] Target genome list was writen to GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:28,004] [INFO] Task started: fastANI
[2024-01-24 14:40:28,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg23eb8fc0-66cd-478a-8c9c-367848805a48/GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna.gz --refList GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:43,912] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:43,954] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:43,954] [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_900128905.1	s__Bacteroides_G luti	100.0	1353	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015654535.1	s__Bacteroides_G sp015654535	78.1376	399	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865075.1	s__Bacteroides faecalis	77.6347	145	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210075.1	s__Bacteroides xylanisolvens	77.5708	120	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_900106755.1	s__Bacteroides faecis	77.5282	131	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_010500995.1	s__Bacteroides_H sp010500995	77.5075	104	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003438995.1	s__OM05-12 sp003438995	77.5074	144	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__OM05-12	95.0	99.98	99.97	0.96	0.89	4	-
GCF_009193295.2	s__Bacteroides luhongzhouii	77.4581	142	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	77.4008	132	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCA_902362375.1	s__Bacteroides sp902362375	77.3612	138	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_000613385.1	s__Bacteroides acidifaciens	77.3464	106	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_900104585.1	s__Bacteroides ihuae	77.2435	151	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902364365.1	s__Bacteroides sp900556215	77.1451	138	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_000614125.1	s__Bacteroides rodentium	77.1402	85	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500955.1	s__Bacteroides_H sp010500955	77.1369	115	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007896885.1	s__Bacteroides sp007896885	76.8032	101	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.28	98.56	0.94	0.88	3	-
GCA_900552645.1	s__Phocaeicola sp900552645	76.7027	79	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762525.1	s__Bacteroides sp900762525	76.1355	107	1354	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:43,956] [INFO] GTDB search result was written to GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:43,957] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:43,961] [INFO] DFAST_QC result json was written to GCF_900128905.1_IMG-taxon_2695420932_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:40:43,962] [INFO] DFAST_QC completed!
[2024-01-24 14:40:43,962] [INFO] Total running time: 0h1m43s