[2023-06-28 19:48:20,581] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:20,584] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:20,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference
[2023-06-28 19:48:21,854] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:21,855] [INFO] Task started: Prodigal
[2023-06-28 19:48:21,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c9ada3f-4808-47a3-aa12-2934d463e3ed/GCA_944322285.1_BRZ_KF_bin27_genomic.fna.gz | prodigal -d GCA_944322285.1_BRZ_KF_bin27_genomic.fna/cds.fna -a GCA_944322285.1_BRZ_KF_bin27_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:43,416] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:43,417] [INFO] Task started: HMMsearch
[2023-06-28 19:48:43,417] [INFO] Running command: hmmsearch --tblout GCA_944322285.1_BRZ_KF_bin27_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference/reference_markers.hmm GCA_944322285.1_BRZ_KF_bin27_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:43,658] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:43,659] [INFO] Found 6/6 markers.
[2023-06-28 19:48:43,693] [INFO] Query marker FASTA was written to GCA_944322285.1_BRZ_KF_bin27_genomic.fna/markers.fasta
[2023-06-28 19:48:43,693] [INFO] Task started: Blastn
[2023-06-28 19:48:43,693] [INFO] Running command: blastn -query GCA_944322285.1_BRZ_KF_bin27_genomic.fna/markers.fasta -db /var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference/reference_markers.fasta -out GCA_944322285.1_BRZ_KF_bin27_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:44,289] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:44,293] [INFO] Selected 24 target genomes.
[2023-06-28 19:48:44,293] [INFO] Target genome list was writen to GCA_944322285.1_BRZ_KF_bin27_genomic.fna/target_genomes.txt
[2023-06-28 19:48:44,376] [INFO] Task started: fastANI
[2023-06-28 19:48:44,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c9ada3f-4808-47a3-aa12-2934d463e3ed/GCA_944322285.1_BRZ_KF_bin27_genomic.fna.gz --refList GCA_944322285.1_BRZ_KF_bin27_genomic.fna/target_genomes.txt --output GCA_944322285.1_BRZ_KF_bin27_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:58,975] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:58,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:58,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:58,990] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:58,991] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:48:58,991] [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 stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	77.9146	205	1187	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	77.8603	204	1187	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	77.8555	209	1187	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	77.803	201	1187	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	77.7692	205	1187	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	77.7256	215	1187	95	below_threshold
Bacteroides heparinolyticus	strain=DSM 23917	GCA_004342845.1	28113	28113	type	True	77.6943	180	1187	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.6526	216	1187	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	77.6398	219	1187	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	77.6292	219	1187	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	77.6107	212	1187	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	77.5924	185	1187	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	77.5479	197	1187	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	77.4566	202	1187	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	77.3647	166	1187	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	77.2732	180	1187	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.1861	92	1187	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:58,993] [INFO] DFAST Taxonomy check result was written to GCA_944322285.1_BRZ_KF_bin27_genomic.fna/tc_result.tsv
[2023-06-28 19:48:58,994] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:58,994] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:58,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference/checkm_data
[2023-06-28 19:48:58,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:59,035] [INFO] Task started: CheckM
[2023-06-28 19:48:59,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322285.1_BRZ_KF_bin27_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322285.1_BRZ_KF_bin27_genomic.fna/checkm_input GCA_944322285.1_BRZ_KF_bin27_genomic.fna/checkm_result
[2023-06-28 19:49:57,830] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:57,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:57,849] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:57,849] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:57,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322285.1_BRZ_KF_bin27_genomic.fna/markers.fasta)
[2023-06-28 19:49:57,849] [INFO] Task started: Blastn
[2023-06-28 19:49:57,849] [INFO] Running command: blastn -query GCA_944322285.1_BRZ_KF_bin27_genomic.fna/markers.fasta -db /var/lib/cwl/stgad7f49b8-a990-434e-9b4b-5198668c61e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322285.1_BRZ_KF_bin27_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:58,653] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:58,657] [INFO] Selected 18 target genomes.
[2023-06-28 19:49:58,657] [INFO] Target genome list was writen to GCA_944322285.1_BRZ_KF_bin27_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:58,687] [INFO] Task started: fastANI
[2023-06-28 19:49:58,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c9ada3f-4808-47a3-aa12-2934d463e3ed/GCA_944322285.1_BRZ_KF_bin27_genomic.fna.gz --refList GCA_944322285.1_BRZ_KF_bin27_genomic.fna/target_genomes_gtdb.txt --output GCA_944322285.1_BRZ_KF_bin27_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:50:10,370] [INFO] Task succeeded: fastANI
[2023-06-28 19:50:10,384] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:50:10,384] [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_900128475.1	s__Bacteroides massiliensis	79.0653	406	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCA_019115825.1	s__Bacteroides pullicola	79.0438	272	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130135.1	s__Bacteroides togonis	78.8276	336	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCA_019116285.1	s__Bacteroides merdigallinarum	78.7446	252	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118325.1	s__Bacteroides intestinavium	78.6248	244	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116805.1	s__Bacteroides merdavium	78.5684	312	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	78.2219	234	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108345.1	s__Bacteroides ndongoniae	78.0964	295	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCA_905201685.1	s__Bacteroides sp905201685	78.0486	126	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553815.1	s__Bacteroides sp900553815	77.9261	208	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCF_000374365.1	s__Bacteroides gallinarum	77.8555	209	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017471925.1	s__Bacteroides sp017471925	77.7357	202	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154205.1	s__Bacteroides uniformis	77.7212	214	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_004342845.1	s__Bacteroides heparinolyticus	77.7058	180	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_000186225.1	s__Bacteroides helcogenes	77.5598	173	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	77.5151	198	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCA_910578895.1	s__Bacteroides sp910578895	77.4533	194	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158035.1	s__Bacteroides cellulosilyticus	77.3619	167	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	-
--------------------------------------------------------------------------------
[2023-06-28 19:50:10,386] [INFO] GTDB search result was written to GCA_944322285.1_BRZ_KF_bin27_genomic.fna/result_gtdb.tsv
[2023-06-28 19:50:10,387] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:50:10,391] [INFO] DFAST_QC result json was written to GCA_944322285.1_BRZ_KF_bin27_genomic.fna/dqc_result.json
[2023-06-28 19:50:10,391] [INFO] DFAST_QC completed!
[2023-06-28 19:50:10,391] [INFO] Total running time: 0h1m50s