[2024-01-25 20:14:36,036] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:36,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:36,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference
[2024-01-25 20:14:37,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:37,223] [INFO] Task started: Prodigal
[2024-01-25 20:14:37,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1b9b83c-3811-49da-a09b-b55dc0324004/GCF_016918765.2_ASM1691876v2_genomic.fna.gz | prodigal -d GCF_016918765.2_ASM1691876v2_genomic.fna/cds.fna -a GCF_016918765.2_ASM1691876v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:47,578] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:47,579] [INFO] Task started: HMMsearch
[2024-01-25 20:14:47,579] [INFO] Running command: hmmsearch --tblout GCF_016918765.2_ASM1691876v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference/reference_markers.hmm GCF_016918765.2_ASM1691876v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:47,787] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:47,788] [INFO] Found 6/6 markers.
[2024-01-25 20:14:47,817] [INFO] Query marker FASTA was written to GCF_016918765.2_ASM1691876v2_genomic.fna/markers.fasta
[2024-01-25 20:14:47,817] [INFO] Task started: Blastn
[2024-01-25 20:14:47,817] [INFO] Running command: blastn -query GCF_016918765.2_ASM1691876v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference/reference_markers.fasta -out GCF_016918765.2_ASM1691876v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:48,520] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:48,525] [INFO] Selected 33 target genomes.
[2024-01-25 20:14:48,525] [INFO] Target genome list was writen to GCF_016918765.2_ASM1691876v2_genomic.fna/target_genomes.txt
[2024-01-25 20:14:48,578] [INFO] Task started: fastANI
[2024-01-25 20:14:48,579] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1b9b83c-3811-49da-a09b-b55dc0324004/GCF_016918765.2_ASM1691876v2_genomic.fna.gz --refList GCF_016918765.2_ASM1691876v2_genomic.fna/target_genomes.txt --output GCF_016918765.2_ASM1691876v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:14,764] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:14,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:14,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:14,781] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:14,782] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:14,782] [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
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	100.0	1202	1202	95	conclusive
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	78.6645	357	1202	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	78.3725	292	1202	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	78.0028	365	1202	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	77.9406	306	1202	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.8069	257	1202	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	77.8035	208	1202	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.7352	255	1202	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	77.6998	324	1202	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	77.4455	243	1202	95	below_threshold
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	77.4062	244	1202	95	below_threshold
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	76.9801	72	1202	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	76.5814	100	1202	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	76.4319	127	1202	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.3241	148	1202	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.2897	148	1202	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.2838	95	1202	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	76.2755	116	1202	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.2043	135	1202	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.0616	152	1202	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	76.0422	130	1202	95	below_threshold
Pseudomarimonas arenosa	strain=CAU 1598	GCA_014841215.1	2774145	2774145	type	True	76.0273	65	1202	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	75.9134	86	1202	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	75.7509	104	1202	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	75.6282	51	1202	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	75.4443	51	1202	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	75.4346	72	1202	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	75.3422	75	1202	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	75.2309	62	1202	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	75.1275	60	1202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:14,786] [INFO] DFAST Taxonomy check result was written to GCF_016918765.2_ASM1691876v2_genomic.fna/tc_result.tsv
[2024-01-25 20:15:14,787] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:14,787] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:14,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference/checkm_data
[2024-01-25 20:15:14,788] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:14,832] [INFO] Task started: CheckM
[2024-01-25 20:15:14,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918765.2_ASM1691876v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918765.2_ASM1691876v2_genomic.fna/checkm_input GCF_016918765.2_ASM1691876v2_genomic.fna/checkm_result
[2024-01-25 20:16:00,745] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:00,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:00,764] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:00,764] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:00,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918765.2_ASM1691876v2_genomic.fna/markers.fasta)
[2024-01-25 20:16:00,765] [INFO] Task started: Blastn
[2024-01-25 20:16:00,765] [INFO] Running command: blastn -query GCF_016918765.2_ASM1691876v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg495f3949-30ed-44fd-ab9f-6e110ca6e08c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918765.2_ASM1691876v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:01,993] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:01,995] [INFO] Selected 26 target genomes.
[2024-01-25 20:16:01,996] [INFO] Target genome list was writen to GCF_016918765.2_ASM1691876v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:02,015] [INFO] Task started: fastANI
[2024-01-25 20:16:02,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1b9b83c-3811-49da-a09b-b55dc0324004/GCF_016918765.2_ASM1691876v2_genomic.fna.gz --refList GCF_016918765.2_ASM1691876v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016918765.2_ASM1691876v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:18,528] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:18,540] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:18,540] [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_016918765.1	s__Polycyclovorans sp016918765	100.0	1202	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002706265.1	s__Polycyclovorans sp002706265	79.1758	352	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	99.22	98.54	0.87	0.78	3	-
GCF_000711245.1	s__Polycyclovorans algicola	78.6257	356	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	78.4566	350	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	78.2942	377	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	78.0172	335	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930645.1	s__Solimonas_A fluminis	78.0012	365	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	77.9505	282	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	77.8289	257	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.8223	289	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	77.7462	255	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047655.1	s__CAU-1509 sp005047655	77.6853	256	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__CAU-1509	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	77.6793	323	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	77.3051	170	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196875.2	s__Halomonas elongata	76.8562	71	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	-
GCA_017305095.1	s__Thermomonas sp017305095	76.3294	111	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008725655.1	s__W260 sp008725655	76.1673	80	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-36;g__W260	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	75.8339	120	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	75.202	85	1202	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:18,546] [INFO] GTDB search result was written to GCF_016918765.2_ASM1691876v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:18,546] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:18,550] [INFO] DFAST_QC result json was written to GCF_016918765.2_ASM1691876v2_genomic.fna/dqc_result.json
[2024-01-25 20:16:18,551] [INFO] DFAST_QC completed!
[2024-01-25 20:16:18,551] [INFO] Total running time: 0h1m43s