[2023-06-08 20:36:18,523] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:18,525] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:18,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference
[2023-06-08 20:36:20,092] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:20,093] [INFO] Task started: Prodigal
[2023-06-08 20:36:20,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg39f78b3b-023c-4480-8e09-5149f2f13951/GCA_947581665.1_Lapin-001_bin20_genomic.fna.gz | prodigal -d GCA_947581665.1_Lapin-001_bin20_genomic.fna/cds.fna -a GCA_947581665.1_Lapin-001_bin20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:24,627] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:24,627] [INFO] Task started: HMMsearch
[2023-06-08 20:36:24,627] [INFO] Running command: hmmsearch --tblout GCA_947581665.1_Lapin-001_bin20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference/reference_markers.hmm GCA_947581665.1_Lapin-001_bin20_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:24,853] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:24,854] [INFO] Found 6/6 markers.
[2023-06-08 20:36:24,886] [INFO] Query marker FASTA was written to GCA_947581665.1_Lapin-001_bin20_genomic.fna/markers.fasta
[2023-06-08 20:36:24,887] [INFO] Task started: Blastn
[2023-06-08 20:36:24,887] [INFO] Running command: blastn -query GCA_947581665.1_Lapin-001_bin20_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference/reference_markers.fasta -out GCA_947581665.1_Lapin-001_bin20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:25,618] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:25,622] [INFO] Selected 22 target genomes.
[2023-06-08 20:36:25,622] [INFO] Target genome list was writen to GCA_947581665.1_Lapin-001_bin20_genomic.fna/target_genomes.txt
[2023-06-08 20:36:25,646] [INFO] Task started: fastANI
[2023-06-08 20:36:25,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f78b3b-023c-4480-8e09-5149f2f13951/GCA_947581665.1_Lapin-001_bin20_genomic.fna.gz --refList GCA_947581665.1_Lapin-001_bin20_genomic.fna/target_genomes.txt --output GCA_947581665.1_Lapin-001_bin20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:42,896] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:42,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:42,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:42,908] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:42,908] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:42,908] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	78.0553	99	441	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.0025	95	441	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	77.9449	114	441	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	77.8475	97	441	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	77.7415	92	441	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	77.6216	96	441	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	77.5828	87	441	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	77.5473	65	441	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	77.5372	68	441	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	77.5317	80	441	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	76.9988	65	441	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	76.7389	67	441	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	76.7186	68	441	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:42,910] [INFO] DFAST Taxonomy check result was written to GCA_947581665.1_Lapin-001_bin20_genomic.fna/tc_result.tsv
[2023-06-08 20:36:42,911] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:42,911] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:42,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference/checkm_data
[2023-06-08 20:36:42,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:42,934] [INFO] Task started: CheckM
[2023-06-08 20:36:42,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947581665.1_Lapin-001_bin20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947581665.1_Lapin-001_bin20_genomic.fna/checkm_input GCA_947581665.1_Lapin-001_bin20_genomic.fna/checkm_result
[2023-06-08 20:37:02,796] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:02,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:02,817] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:02,817] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:02,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947581665.1_Lapin-001_bin20_genomic.fna/markers.fasta)
[2023-06-08 20:37:02,818] [INFO] Task started: Blastn
[2023-06-08 20:37:02,818] [INFO] Running command: blastn -query GCA_947581665.1_Lapin-001_bin20_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb5a362b-2fd5-4843-a4f6-f5bb3dc49641/dqc_reference/reference_markers_gtdb.fasta -out GCA_947581665.1_Lapin-001_bin20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:03,956] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:03,962] [INFO] Selected 26 target genomes.
[2023-06-08 20:37:03,962] [INFO] Target genome list was writen to GCA_947581665.1_Lapin-001_bin20_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:04,101] [INFO] Task started: fastANI
[2023-06-08 20:37:04,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f78b3b-023c-4480-8e09-5149f2f13951/GCA_947581665.1_Lapin-001_bin20_genomic.fna.gz --refList GCA_947581665.1_Lapin-001_bin20_genomic.fna/target_genomes_gtdb.txt --output GCA_947581665.1_Lapin-001_bin20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:16,353] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:16,370] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 20:37:16,371] [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_004793665.1	s__NM07-P-09 sp004793665	78.877	125	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__NM07-P-09	95.0	99.12	98.60	0.95	0.93	6	-
GCF_002160255.1	s__Thermophilibacter avistercoris	78.1133	103	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.79	97.22	0.93	0.92	5	-
GCA_900549525.1	s__Parolsenella sp900549525	78.0225	73	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.58	99.58	0.87	0.87	2	-
GCF_016900775.1	s__Thermophilibacter uli_A	78.0151	119	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901212675.1	s__Parolsenella uli_B	77.9756	98	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.31	96.31	0.90	0.90	2	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	77.9449	114	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900315.1	s__Thermophilibacter profusa_A	77.9033	98	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159495.1	s__Thermophilibacter sp002159495	77.8799	102	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	77.8446	103	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCA_902795065.1	s__RUG721 sp900321745	77.8228	94	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
GCA_015062715.1	s__SIG37 sp015062715	77.8086	81	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__SIG37	95.0	96.94	96.94	0.73	0.73	2	-
GCA_019117005.1	s__Collinsella stercoripullorum	77.6832	75	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.76	98.76	0.91	0.91	2	-
GCF_003966955.1	s__Parolsenella catena	77.6197	86	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.03	97.75	0.95	0.92	5	-
GCA_003862195.1	s__Parafannyhessea sp003862195	77.563	84	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_902780325.1	s__Parafannyhessea sp902787335	77.5352	85	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCA_002331575.1	s__Olsenella_D sp002331575	77.3836	83	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314575.1	s__UBA7741 sp900314575	77.2054	95	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCA_902782635.1	s__CACZNT01 sp902782635	76.8206	88	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__CACZNT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793195.1	s__RUG440 sp902793195	76.7141	57	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715125.1	s__Coprousia avicola	76.6373	82	441	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Coprousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:16,373] [INFO] GTDB search result was written to GCA_947581665.1_Lapin-001_bin20_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:16,373] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:16,378] [INFO] DFAST_QC result json was written to GCA_947581665.1_Lapin-001_bin20_genomic.fna/dqc_result.json
[2023-06-08 20:37:16,378] [INFO] DFAST_QC completed!
[2023-06-08 20:37:16,379] [INFO] Total running time: 0h0m58s