[2023-06-18 19:17:05,488] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:17:05,490] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:17:05,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference
[2023-06-18 19:17:06,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:17:06,798] [INFO] Task started: Prodigal
[2023-06-18 19:17:06,799] [INFO] Running command: gunzip -c /var/lib/cwl/stgbafb1f90-a169-4315-8dad-c7599e8fc52b/GCA_018883965.1_ASM1888396v1_genomic.fna.gz | prodigal -d GCA_018883965.1_ASM1888396v1_genomic.fna/cds.fna -a GCA_018883965.1_ASM1888396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:17:25,012] [INFO] Task succeeded: Prodigal
[2023-06-18 19:17:25,012] [INFO] Task started: HMMsearch
[2023-06-18 19:17:25,012] [INFO] Running command: hmmsearch --tblout GCA_018883965.1_ASM1888396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference/reference_markers.hmm GCA_018883965.1_ASM1888396v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:17:25,312] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:17:25,313] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbafb1f90-a169-4315-8dad-c7599e8fc52b/GCA_018883965.1_ASM1888396v1_genomic.fna.gz]
[2023-06-18 19:17:25,343] [INFO] Query marker FASTA was written to GCA_018883965.1_ASM1888396v1_genomic.fna/markers.fasta
[2023-06-18 19:17:25,343] [INFO] Task started: Blastn
[2023-06-18 19:17:25,344] [INFO] Running command: blastn -query GCA_018883965.1_ASM1888396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference/reference_markers.fasta -out GCA_018883965.1_ASM1888396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:25,936] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:25,940] [INFO] Selected 18 target genomes.
[2023-06-18 19:17:25,940] [INFO] Target genome list was writen to GCA_018883965.1_ASM1888396v1_genomic.fna/target_genomes.txt
[2023-06-18 19:17:25,941] [INFO] Task started: fastANI
[2023-06-18 19:17:25,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafb1f90-a169-4315-8dad-c7599e8fc52b/GCA_018883965.1_ASM1888396v1_genomic.fna.gz --refList GCA_018883965.1_ASM1888396v1_genomic.fna/target_genomes.txt --output GCA_018883965.1_ASM1888396v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:17:37,722] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:37,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:17:37,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:17:37,737] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:17:37,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:17:37,738] [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 plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	83.492	651	1037	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.4797	331	1037	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	79.3826	341	1037	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.3172	314	1037	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.9903	282	1037	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.9412	278	1037	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	78.6309	242	1037	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.4763	252	1037	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	78.0203	231	1037	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	77.6532	162	1037	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	77.5384	123	1037	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.3419	125	1037	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	77.2835	165	1037	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	77.248	167	1037	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	77.1631	99	1037	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.1158	124	1037	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	77.027	117	1037	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	76.956	121	1037	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:17:37,750] [INFO] DFAST Taxonomy check result was written to GCA_018883965.1_ASM1888396v1_genomic.fna/tc_result.tsv
[2023-06-18 19:17:37,750] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:17:37,751] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:17:37,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference/checkm_data
[2023-06-18 19:17:37,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:17:37,789] [INFO] Task started: CheckM
[2023-06-18 19:17:37,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018883965.1_ASM1888396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018883965.1_ASM1888396v1_genomic.fna/checkm_input GCA_018883965.1_ASM1888396v1_genomic.fna/checkm_result
[2023-06-18 19:18:30,968] [INFO] Task succeeded: CheckM
[2023-06-18 19:18:30,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 19:18:30,991] [INFO] ===== Completeness check finished =====
[2023-06-18 19:18:30,992] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:18:30,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018883965.1_ASM1888396v1_genomic.fna/markers.fasta)
[2023-06-18 19:18:30,993] [INFO] Task started: Blastn
[2023-06-18 19:18:30,993] [INFO] Running command: blastn -query GCA_018883965.1_ASM1888396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89039882-a6a0-4739-8025-11a0171b6a0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018883965.1_ASM1888396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:18:31,791] [INFO] Task succeeded: Blastn
[2023-06-18 19:18:31,796] [INFO] Selected 7 target genomes.
[2023-06-18 19:18:31,796] [INFO] Target genome list was writen to GCA_018883965.1_ASM1888396v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:18:31,802] [INFO] Task started: fastANI
[2023-06-18 19:18:31,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgbafb1f90-a169-4315-8dad-c7599e8fc52b/GCA_018883965.1_ASM1888396v1_genomic.fna.gz --refList GCA_018883965.1_ASM1888396v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018883965.1_ASM1888396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:18:37,329] [INFO] Task succeeded: fastANI
[2023-06-18 19:18:37,343] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:18:37,343] [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_902362595.1	s__Phocaeicola merdigallinarum	98.6145	900	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	conclusive
GCF_900128455.1	s__Phocaeicola mediterraneensis	91.7144	776	1037	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	90.7935	626	1037	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	89.344	578	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900355.1	s__Phocaeicola sp900551065	88.8024	721	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_000187895.1	s__Phocaeicola plebeius	83.492	651	1037	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	83.4241	638	1037	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
--------------------------------------------------------------------------------
[2023-06-18 19:18:37,346] [INFO] GTDB search result was written to GCA_018883965.1_ASM1888396v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:18:37,347] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:18:37,353] [INFO] DFAST_QC result json was written to GCA_018883965.1_ASM1888396v1_genomic.fna/dqc_result.json
[2023-06-18 19:18:37,353] [INFO] DFAST_QC completed!
[2023-06-18 19:18:37,353] [INFO] Total running time: 0h1m32s