[2023-06-28 21:14:07,225] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:14:07,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:14:07,228] [INFO] DQC Reference Directory: /var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference
[2023-06-28 21:14:09,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:14:09,584] [INFO] Task started: Prodigal
[2023-06-28 21:14:09,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg5502538f-52d1-402c-aa0b-55af9be0419a/GCA_944320735.1_E30_bin188_genomic.fna.gz | prodigal -d GCA_944320735.1_E30_bin188_genomic.fna/cds.fna -a GCA_944320735.1_E30_bin188_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:14:26,737] [INFO] Task succeeded: Prodigal
[2023-06-28 21:14:26,738] [INFO] Task started: HMMsearch
[2023-06-28 21:14:26,738] [INFO] Running command: hmmsearch --tblout GCA_944320735.1_E30_bin188_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference/reference_markers.hmm GCA_944320735.1_E30_bin188_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:14:26,976] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:14:26,978] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5502538f-52d1-402c-aa0b-55af9be0419a/GCA_944320735.1_E30_bin188_genomic.fna.gz]
[2023-06-28 21:14:27,008] [INFO] Query marker FASTA was written to GCA_944320735.1_E30_bin188_genomic.fna/markers.fasta
[2023-06-28 21:14:27,009] [INFO] Task started: Blastn
[2023-06-28 21:14:27,009] [INFO] Running command: blastn -query GCA_944320735.1_E30_bin188_genomic.fna/markers.fasta -db /var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference/reference_markers.fasta -out GCA_944320735.1_E30_bin188_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:14:27,597] [INFO] Task succeeded: Blastn
[2023-06-28 21:14:27,601] [INFO] Selected 22 target genomes.
[2023-06-28 21:14:27,601] [INFO] Target genome list was writen to GCA_944320735.1_E30_bin188_genomic.fna/target_genomes.txt
[2023-06-28 21:14:27,603] [INFO] Task started: fastANI
[2023-06-28 21:14:27,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg5502538f-52d1-402c-aa0b-55af9be0419a/GCA_944320735.1_E30_bin188_genomic.fna.gz --refList GCA_944320735.1_E30_bin188_genomic.fna/target_genomes.txt --output GCA_944320735.1_E30_bin188_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:14:42,160] [INFO] Task succeeded: fastANI
[2023-06-28 21:14:42,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:14:42,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:14:42,179] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:14:42,179] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:14:42,179] [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 uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	77.6313	152	849	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	77.6259	153	849	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	77.6213	154	849	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	77.6026	155	849	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.3652	154	849	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	77.3437	148	849	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	77.2185	130	849	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	77.2167	166	849	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	77.2047	144	849	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	77.1352	152	849	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.0769	65	849	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	76.9299	128	849	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	76.8849	128	849	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	76.7987	110	849	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	76.7041	51	849	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	76.6855	111	849	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	76.6694	51	849	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	76.5742	89	849	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	76.5563	91	849	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	76.3457	57	849	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:14:42,181] [INFO] DFAST Taxonomy check result was written to GCA_944320735.1_E30_bin188_genomic.fna/tc_result.tsv
[2023-06-28 21:14:42,182] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:14:42,182] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:14:42,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference/checkm_data
[2023-06-28 21:14:42,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:14:42,216] [INFO] Task started: CheckM
[2023-06-28 21:14:42,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320735.1_E30_bin188_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320735.1_E30_bin188_genomic.fna/checkm_input GCA_944320735.1_E30_bin188_genomic.fna/checkm_result
[2023-06-28 21:15:31,446] [INFO] Task succeeded: CheckM
[2023-06-28 21:15:31,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:15:31,469] [INFO] ===== Completeness check finished =====
[2023-06-28 21:15:31,470] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:15:31,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320735.1_E30_bin188_genomic.fna/markers.fasta)
[2023-06-28 21:15:31,470] [INFO] Task started: Blastn
[2023-06-28 21:15:31,471] [INFO] Running command: blastn -query GCA_944320735.1_E30_bin188_genomic.fna/markers.fasta -db /var/lib/cwl/stg13513243-e51b-4a58-b7d3-785ffe1642e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320735.1_E30_bin188_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:15:32,302] [INFO] Task succeeded: Blastn
[2023-06-28 21:15:32,306] [INFO] Selected 13 target genomes.
[2023-06-28 21:15:32,306] [INFO] Target genome list was writen to GCA_944320735.1_E30_bin188_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:15:32,313] [INFO] Task started: fastANI
[2023-06-28 21:15:32,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5502538f-52d1-402c-aa0b-55af9be0419a/GCA_944320735.1_E30_bin188_genomic.fna.gz --refList GCA_944320735.1_E30_bin188_genomic.fna/target_genomes_gtdb.txt --output GCA_944320735.1_E30_bin188_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:15:39,786] [INFO] Task succeeded: fastANI
[2023-06-28 21:15:39,803] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:15:39,803] [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	78.8136	290	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCF_900130135.1	s__Bacteroides togonis	78.4885	248	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCA_019115825.1	s__Bacteroides pullicola	78.4223	218	849	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	78.3612	232	849	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	78.0813	190	849	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	77.9386	185	849	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	77.7726	198	849	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	77.761	227	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
GCF_000154205.1	s__Bacteroides uniformis	77.6432	153	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_002160055.1	s__Bacteroides avicola	77.5813	189	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.46	98.46	0.91	0.91	2	-
GCA_900553815.1	s__Bacteroides sp900553815	77.5327	154	849	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	77.3175	139	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	76.9692	155	849	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
--------------------------------------------------------------------------------
[2023-06-28 21:15:39,805] [INFO] GTDB search result was written to GCA_944320735.1_E30_bin188_genomic.fna/result_gtdb.tsv
[2023-06-28 21:15:39,805] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:15:39,809] [INFO] DFAST_QC result json was written to GCA_944320735.1_E30_bin188_genomic.fna/dqc_result.json
[2023-06-28 21:15:39,809] [INFO] DFAST_QC completed!
[2023-06-28 21:15:39,809] [INFO] Total running time: 0h1m33s