[2023-06-28 17:16:01,801] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:16:01,803] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:16:01,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference
[2023-06-28 17:16:03,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:16:03,069] [INFO] Task started: Prodigal
[2023-06-28 17:16:03,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg2009c43e-1892-4f04-b8cd-4e8b22aebb64/GCA_944320005.1_BRZ_BD_bin71_genomic.fna.gz | prodigal -d GCA_944320005.1_BRZ_BD_bin71_genomic.fna/cds.fna -a GCA_944320005.1_BRZ_BD_bin71_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:16:19,191] [INFO] Task succeeded: Prodigal
[2023-06-28 17:16:19,191] [INFO] Task started: HMMsearch
[2023-06-28 17:16:19,192] [INFO] Running command: hmmsearch --tblout GCA_944320005.1_BRZ_BD_bin71_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference/reference_markers.hmm GCA_944320005.1_BRZ_BD_bin71_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:16:19,467] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:16:19,469] [INFO] Found 6/6 markers.
[2023-06-28 17:16:19,504] [INFO] Query marker FASTA was written to GCA_944320005.1_BRZ_BD_bin71_genomic.fna/markers.fasta
[2023-06-28 17:16:19,505] [INFO] Task started: Blastn
[2023-06-28 17:16:19,505] [INFO] Running command: blastn -query GCA_944320005.1_BRZ_BD_bin71_genomic.fna/markers.fasta -db /var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference/reference_markers.fasta -out GCA_944320005.1_BRZ_BD_bin71_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:16:20,109] [INFO] Task succeeded: Blastn
[2023-06-28 17:16:20,114] [INFO] Selected 18 target genomes.
[2023-06-28 17:16:20,114] [INFO] Target genome list was writen to GCA_944320005.1_BRZ_BD_bin71_genomic.fna/target_genomes.txt
[2023-06-28 17:16:20,116] [INFO] Task started: fastANI
[2023-06-28 17:16:20,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg2009c43e-1892-4f04-b8cd-4e8b22aebb64/GCA_944320005.1_BRZ_BD_bin71_genomic.fna.gz --refList GCA_944320005.1_BRZ_BD_bin71_genomic.fna/target_genomes.txt --output GCA_944320005.1_BRZ_BD_bin71_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:16:31,795] [INFO] Task succeeded: fastANI
[2023-06-28 17:16:31,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:16:31,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:16:31,815] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:16:31,815] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:16:31,816] [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
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	83.3038	675	1079	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	83.3033	695	1079	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.0443	295	1079	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.0117	326	1079	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.0102	335	1079	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.972	344	1079	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.5059	272	1079	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	77.9332	209	1079	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.9312	222	1079	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	77.6218	175	1079	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	77.5841	172	1079	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.3617	117	1079	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	76.8367	126	1079	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	76.8153	112	1079	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002222615.2	47678	47678	suspected-type	True	76.7942	113	1079	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	76.7916	113	1079	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	76.7911	113	1079	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	76.7572	113	1079	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:16:31,819] [INFO] DFAST Taxonomy check result was written to GCA_944320005.1_BRZ_BD_bin71_genomic.fna/tc_result.tsv
[2023-06-28 17:16:31,820] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:16:31,820] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:16:31,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference/checkm_data
[2023-06-28 17:16:31,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:16:31,860] [INFO] Task started: CheckM
[2023-06-28 17:16:31,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320005.1_BRZ_BD_bin71_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320005.1_BRZ_BD_bin71_genomic.fna/checkm_input GCA_944320005.1_BRZ_BD_bin71_genomic.fna/checkm_result
[2023-06-28 17:17:21,799] [INFO] Task succeeded: CheckM
[2023-06-28 17:17:21,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:17:21,823] [INFO] ===== Completeness check finished =====
[2023-06-28 17:17:21,823] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:17:21,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320005.1_BRZ_BD_bin71_genomic.fna/markers.fasta)
[2023-06-28 17:17:21,824] [INFO] Task started: Blastn
[2023-06-28 17:17:21,824] [INFO] Running command: blastn -query GCA_944320005.1_BRZ_BD_bin71_genomic.fna/markers.fasta -db /var/lib/cwl/stg819537e3-e6c9-4a00-9d5c-5883da25fbcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320005.1_BRZ_BD_bin71_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:17:22,651] [INFO] Task succeeded: Blastn
[2023-06-28 17:17:22,656] [INFO] Selected 17 target genomes.
[2023-06-28 17:17:22,656] [INFO] Target genome list was writen to GCA_944320005.1_BRZ_BD_bin71_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:17:22,660] [INFO] Task started: fastANI
[2023-06-28 17:17:22,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg2009c43e-1892-4f04-b8cd-4e8b22aebb64/GCA_944320005.1_BRZ_BD_bin71_genomic.fna.gz --refList GCA_944320005.1_BRZ_BD_bin71_genomic.fna/target_genomes_gtdb.txt --output GCA_944320005.1_BRZ_BD_bin71_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:17:33,006] [INFO] Task succeeded: fastANI
[2023-06-28 17:17:33,026] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:17:33,026] [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
GCA_900553185.1	s__Phocaeicola sp900553185	98.8436	650	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	conclusive
GCF_000374585.1	s__Phocaeicola barnesiae	83.3033	695	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_900551645.1	s__Phocaeicola sp900551645	83.1892	491	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.46	98.46	0.80	0.80	2	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	79.9733	381	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_016900355.1	s__Phocaeicola sp900551065	79.6457	356	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	79.6141	369	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCA_900551445.1	s__Phocaeicola sp900551445	79.3652	286	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.0609	265	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157915.1	s__Phocaeicola coprophilus	79.0102	335	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCF_000187895.1	s__Phocaeicola plebeius	78.9661	345	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_003437535.1	s__Phocaeicola plebeius_A	78.943	334	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCA_000432735.1	s__Phocaeicola sp000432735	78.8354	308	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCA_900542985.1	s__Phocaeicola sp900542985	78.6995	233	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_000436795.1	s__Phocaeicola sp000436795	78.5675	223	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_000154845.1	s__Phocaeicola coprocola	78.4644	274	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCA_900546645.1	s__Phocaeicola sp900546645	77.5224	198	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.94	98.88	0.79	0.75	3	-
GCA_004558305.1	s__Phocaeicola plebeius_B	77.3548	147	1079	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:17:33,029] [INFO] GTDB search result was written to GCA_944320005.1_BRZ_BD_bin71_genomic.fna/result_gtdb.tsv
[2023-06-28 17:17:33,030] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:17:33,034] [INFO] DFAST_QC result json was written to GCA_944320005.1_BRZ_BD_bin71_genomic.fna/dqc_result.json
[2023-06-28 17:17:33,034] [INFO] DFAST_QC completed!
[2023-06-28 17:17:33,035] [INFO] Total running time: 0h1m31s