[2024-01-24 13:17:11,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:11,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:11,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference
[2024-01-24 13:17:12,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:12,844] [INFO] Task started: Prodigal
[2024-01-24 13:17:12,844] [INFO] Running command: gunzip -c /var/lib/cwl/stg8933913b-0635-4177-8023-281e53d1213f/GCF_900104585.1_PRJEB16348_genomic.fna.gz | prodigal -d GCF_900104585.1_PRJEB16348_genomic.fna/cds.fna -a GCF_900104585.1_PRJEB16348_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:31,065] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:31,066] [INFO] Task started: HMMsearch
[2024-01-24 13:17:31,066] [INFO] Running command: hmmsearch --tblout GCF_900104585.1_PRJEB16348_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference/reference_markers.hmm GCF_900104585.1_PRJEB16348_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:31,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:31,342] [INFO] Found 6/6 markers.
[2024-01-24 13:17:31,390] [INFO] Query marker FASTA was written to GCF_900104585.1_PRJEB16348_genomic.fna/markers.fasta
[2024-01-24 13:17:31,391] [INFO] Task started: Blastn
[2024-01-24 13:17:31,391] [INFO] Running command: blastn -query GCF_900104585.1_PRJEB16348_genomic.fna/markers.fasta -db /var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference/reference_markers.fasta -out GCF_900104585.1_PRJEB16348_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:31,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:31,981] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:31,982] [INFO] Target genome list was writen to GCF_900104585.1_PRJEB16348_genomic.fna/target_genomes.txt
[2024-01-24 13:17:32,153] [INFO] Task started: fastANI
[2024-01-24 13:17:32,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg8933913b-0635-4177-8023-281e53d1213f/GCF_900104585.1_PRJEB16348_genomic.fna.gz --refList GCF_900104585.1_PRJEB16348_genomic.fna/target_genomes.txt --output GCF_900104585.1_PRJEB16348_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:46,504] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:46,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:46,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:46,518] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:46,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:46,519] [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 ihuae	strain=Marseille-P2824	GCA_900104585.1	1852362	1852362	type	True	100.0	1351	1351	95	conclusive
Bacteroides graminisolvens	strain=JCM 15093	GCA_000613825.1	477666	477666	type	True	78.2188	290	1351	95	below_threshold
Bacteroides graminisolvens	strain=DSM 19988	GCA_000428125.1	477666	477666	type	True	78.163	292	1351	95	below_threshold
Bacteroides neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	77.5421	154	1351	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	77.4943	165	1351	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	77.409	189	1351	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_000226135.2	674529	674529	type	True	77.4022	175	1351	95	below_threshold
Bacteroides luti	strain=DSM 26991	GCA_900128905.1	1297750	1297750	type	True	77.393	149	1351	95	below_threshold
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	77.3204	188	1351	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	77.3095	176	1351	95	below_threshold
Bacteroides reticulotermitis	strain=DSM 105720	GCA_014196955.1	1133319	1133319	type	True	77.2334	144	1351	95	below_threshold
Bacteroides reticulotermitis	strain=JCM 10512	GCA_000517545.1	1133319	1133319	type	True	77.2271	145	1351	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	77.1846	173	1351	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.1666	139	1351	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	77.1629	101	1351	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	77.1624	180	1351	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	76.7187	98	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,521] [INFO] DFAST Taxonomy check result was written to GCF_900104585.1_PRJEB16348_genomic.fna/tc_result.tsv
[2024-01-24 13:17:46,521] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:46,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:46,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference/checkm_data
[2024-01-24 13:17:46,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:46,571] [INFO] Task started: CheckM
[2024-01-24 13:17:46,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104585.1_PRJEB16348_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104585.1_PRJEB16348_genomic.fna/checkm_input GCF_900104585.1_PRJEB16348_genomic.fna/checkm_result
[2024-01-24 13:18:39,863] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:39,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:39,883] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:39,884] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:39,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104585.1_PRJEB16348_genomic.fna/markers.fasta)
[2024-01-24 13:18:39,884] [INFO] Task started: Blastn
[2024-01-24 13:18:39,885] [INFO] Running command: blastn -query GCF_900104585.1_PRJEB16348_genomic.fna/markers.fasta -db /var/lib/cwl/stg946c9c5e-ef7b-4775-ade1-fc3988db95fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104585.1_PRJEB16348_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:40,746] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:40,750] [INFO] Selected 19 target genomes.
[2024-01-24 13:18:40,751] [INFO] Target genome list was writen to GCF_900104585.1_PRJEB16348_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:40,923] [INFO] Task started: fastANI
[2024-01-24 13:18:40,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg8933913b-0635-4177-8023-281e53d1213f/GCF_900104585.1_PRJEB16348_genomic.fna.gz --refList GCF_900104585.1_PRJEB16348_genomic.fna/target_genomes_gtdb.txt --output GCF_900104585.1_PRJEB16348_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:55,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,581] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:55,581] [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_900104585.1	s__Bacteroides ihuae	100.0	1351	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002307035.1	s__Bacteroides sp002307035	88.0241	869	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.69	98.69	0.85	0.85	2	-
GCF_000428125.1	s__Bacteroides graminisolvens	78.1581	293	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.57	97.75	0.90	0.81	13	-
GCF_000499785.1	s__Bacteroides neonati	77.5423	154	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	77.4943	165	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCF_002849695.1	s__Bacteroides fragilis_A	77.4083	174	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCF_900128905.1	s__Bacteroides_G luti	77.3963	149	1351	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_000025985.1	s__Bacteroides fragilis	77.3575	176	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_000381365.1	s__Bacteroides salyersiae	77.354	187	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_900106755.1	s__Bacteroides faecis	77.3095	176	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	77.2939	167	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCA_014385165.1	s__Bacteroides sp014385165	77.2906	152	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCA_017992695.1	s__Bacteroides sp017992695	77.2578	120	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.85	99.79	0.94	0.93	6	-
GCF_010500995.1	s__Bacteroides_H sp010500995	77.2521	125	1351	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_902362375.1	s__Bacteroides sp902362375	77.1559	183	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_010500955.1	s__Bacteroides_H sp010500955	77.1123	109	1351	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_000172175.1	s__Bacteroides intestinalis	77.0676	156	1351	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.18	96.30	0.86	0.76	22	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,583] [INFO] GTDB search result was written to GCF_900104585.1_PRJEB16348_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:55,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:55,587] [INFO] DFAST_QC result json was written to GCF_900104585.1_PRJEB16348_genomic.fna/dqc_result.json
[2024-01-24 13:18:55,587] [INFO] DFAST_QC completed!
[2024-01-24 13:18:55,587] [INFO] Total running time: 0h1m44s