[2023-06-28 07:57:21,245] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:57:21,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:57:21,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference
[2023-06-28 07:57:22,720] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:57:22,720] [INFO] Task started: Prodigal
[2023-06-28 07:57:22,721] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf3bebbb-b443-408c-9fb3-68417406ddb1/GCA_944320295.1_E20_bin320_genomic.fna.gz | prodigal -d GCA_944320295.1_E20_bin320_genomic.fna/cds.fna -a GCA_944320295.1_E20_bin320_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:57:39,829] [INFO] Task succeeded: Prodigal
[2023-06-28 07:57:39,829] [INFO] Task started: HMMsearch
[2023-06-28 07:57:39,830] [INFO] Running command: hmmsearch --tblout GCA_944320295.1_E20_bin320_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference/reference_markers.hmm GCA_944320295.1_E20_bin320_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:57:40,080] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:57:40,082] [INFO] Found 6/6 markers.
[2023-06-28 07:57:40,150] [INFO] Query marker FASTA was written to GCA_944320295.1_E20_bin320_genomic.fna/markers.fasta
[2023-06-28 07:57:40,150] [INFO] Task started: Blastn
[2023-06-28 07:57:40,150] [INFO] Running command: blastn -query GCA_944320295.1_E20_bin320_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference/reference_markers.fasta -out GCA_944320295.1_E20_bin320_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:40,771] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:40,776] [INFO] Selected 32 target genomes.
[2023-06-28 07:57:40,777] [INFO] Target genome list was writen to GCA_944320295.1_E20_bin320_genomic.fna/target_genomes.txt
[2023-06-28 07:57:40,778] [INFO] Task started: fastANI
[2023-06-28 07:57:40,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf3bebbb-b443-408c-9fb3-68417406ddb1/GCA_944320295.1_E20_bin320_genomic.fna.gz --refList GCA_944320295.1_E20_bin320_genomic.fna/target_genomes.txt --output GCA_944320295.1_E20_bin320_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:57:59,044] [INFO] Task succeeded: fastANI
[2023-06-28 07:57:59,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:57:59,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:57:59,070] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:57:59,071] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 07:57:59,071] [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 clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	77.0517	126	785	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	77.0281	127	785	95	below_threshold
Bacteroides heparinolyticus	strain=DSM 23917	GCA_004342845.1	28113	28113	type	True	77.0195	126	785	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	76.9569	158	785	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	76.9304	155	785	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	76.8214	132	785	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_002998435.1	28119	28119	type	True	76.7718	135	785	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	76.7578	62	785	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	76.7559	63	785	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	76.7512	143	785	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	76.7056	142	785	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	76.701	146	785	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	76.6937	104	785	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	76.6571	121	785	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	76.5099	117	785	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	76.4996	118	785	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	76.4996	118	785	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	76.4559	50	785	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	76.4559	50	785	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	76.4559	50	785	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	76.4559	50	785	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	76.3723	114	785	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	75.9761	52	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:57:59,073] [INFO] DFAST Taxonomy check result was written to GCA_944320295.1_E20_bin320_genomic.fna/tc_result.tsv
[2023-06-28 07:57:59,074] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:57:59,074] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:57:59,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference/checkm_data
[2023-06-28 07:57:59,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:57:59,108] [INFO] Task started: CheckM
[2023-06-28 07:57:59,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320295.1_E20_bin320_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320295.1_E20_bin320_genomic.fna/checkm_input GCA_944320295.1_E20_bin320_genomic.fna/checkm_result
[2023-06-28 07:58:46,705] [INFO] Task succeeded: CheckM
[2023-06-28 07:58:46,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:58:46,727] [INFO] ===== Completeness check finished =====
[2023-06-28 07:58:46,727] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:58:46,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320295.1_E20_bin320_genomic.fna/markers.fasta)
[2023-06-28 07:58:46,728] [INFO] Task started: Blastn
[2023-06-28 07:58:46,728] [INFO] Running command: blastn -query GCA_944320295.1_E20_bin320_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fee384a-081b-4d72-b50c-3588330dfc48/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320295.1_E20_bin320_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:58:47,556] [INFO] Task succeeded: Blastn
[2023-06-28 07:58:47,561] [INFO] Selected 24 target genomes.
[2023-06-28 07:58:47,561] [INFO] Target genome list was writen to GCA_944320295.1_E20_bin320_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:58:47,588] [INFO] Task started: fastANI
[2023-06-28 07:58:47,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf3bebbb-b443-408c-9fb3-68417406ddb1/GCA_944320295.1_E20_bin320_genomic.fna.gz --refList GCA_944320295.1_E20_bin320_genomic.fna/target_genomes_gtdb.txt --output GCA_944320295.1_E20_bin320_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:59:00,192] [INFO] Task succeeded: fastANI
[2023-06-28 07:59:00,213] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 07:59:00,213] [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	79.1913	238	785	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	78.9517	235	785	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	78.775	209	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116285.1	s__Bacteroides merdigallinarum	78.6537	223	785	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	78.5667	204	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116045.1	s__Bacteroides merdipullorum	78.3625	189	785	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	78.3573	197	785	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	78.0931	203	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_900291465.1	s__Phocaeicola_A sp900291465	77.8353	105	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.97	97.87	0.87	0.85	4	-
GCA_017471925.1	s__Bacteroides sp017471925	77.6274	174	785	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	77.3406	167	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_910578895.1	s__Bacteroides sp910578895	77.2555	150	785	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	77.0517	126	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_004342845.1	s__Bacteroides heparinolyticus	77.0195	126	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCA_902388495.1	s__Bacteroides sp902388495	77.0112	135	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_017464815.1	s__Phocaeicola_A sp017464815	76.9861	78	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	76.9589	157	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_002998435.1	s__Bacteroides zoogleoformans	76.7718	135	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003438615.1	s__Bacteroides sp003545565	76.7041	103	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000195635.1	s__Bacteroides fluxus	76.6571	121	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_000155815.1	s__Bacteroides eggerthii	76.5099	117	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCA_017478085.1	s__Prevotella sp017478085	76.2654	51	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521285.1	s__Phocaeicola_A sp017521285	76.2339	51	785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.09	97.09	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-28 07:59:00,215] [INFO] GTDB search result was written to GCA_944320295.1_E20_bin320_genomic.fna/result_gtdb.tsv
[2023-06-28 07:59:00,216] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:59:00,220] [INFO] DFAST_QC result json was written to GCA_944320295.1_E20_bin320_genomic.fna/dqc_result.json
[2023-06-28 07:59:00,221] [INFO] DFAST_QC completed!
[2023-06-28 07:59:00,221] [INFO] Total running time: 0h1m39s