[2024-01-24 13:01:19,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:19,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:19,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference
[2024-01-24 13:01:20,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:20,361] [INFO] Task started: Prodigal
[2024-01-24 13:01:20,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f8d4b43-d4fa-4673-ab18-5a7ab56b7718/GCF_000711245.1_ASM71124v1_genomic.fna.gz | prodigal -d GCF_000711245.1_ASM71124v1_genomic.fna/cds.fna -a GCF_000711245.1_ASM71124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:32,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:32,656] [INFO] Task started: HMMsearch
[2024-01-24 13:01:32,656] [INFO] Running command: hmmsearch --tblout GCF_000711245.1_ASM71124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference/reference_markers.hmm GCF_000711245.1_ASM71124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:32,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:32,926] [INFO] Found 6/6 markers.
[2024-01-24 13:01:32,962] [INFO] Query marker FASTA was written to GCF_000711245.1_ASM71124v1_genomic.fna/markers.fasta
[2024-01-24 13:01:32,963] [INFO] Task started: Blastn
[2024-01-24 13:01:32,963] [INFO] Running command: blastn -query GCF_000711245.1_ASM71124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference/reference_markers.fasta -out GCF_000711245.1_ASM71124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:33,737] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:33,742] [INFO] Selected 23 target genomes.
[2024-01-24 13:01:33,742] [INFO] Target genome list was writen to GCF_000711245.1_ASM71124v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:33,765] [INFO] Task started: fastANI
[2024-01-24 13:01:33,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f8d4b43-d4fa-4673-ab18-5a7ab56b7718/GCF_000711245.1_ASM71124v1_genomic.fna.gz --refList GCF_000711245.1_ASM71124v1_genomic.fna/target_genomes.txt --output GCF_000711245.1_ASM71124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:48,221] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:48,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:48,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:48,243] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:48,243] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:48,243] [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
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	100.0	1217	1217	95	conclusive
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	78.7068	347	1217	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	77.7263	292	1217	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	77.3238	232	1217	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	77.2815	247	1217	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	77.2626	290	1217	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	77.1727	286	1217	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	77.1708	226	1217	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	77.1104	236	1217	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	76.8263	191	1217	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.7665	80	1217	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.611	106	1217	95	below_threshold
Stenotrophobium rhamnosiphilum	strain=GT1R17	GCA_003052265.1	2029166	2029166	type	True	76.5619	96	1217	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.5555	117	1217	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	76.4503	121	1217	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	76.3711	87	1217	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.3068	96	1217	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.2603	104	1217	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	76.1637	101	1217	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	76.1493	106	1217	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.1102	157	1217	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	76.0864	95	1217	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.7719	106	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:48,245] [INFO] DFAST Taxonomy check result was written to GCF_000711245.1_ASM71124v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:48,246] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:48,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:48,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference/checkm_data
[2024-01-24 13:01:48,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:48,290] [INFO] Task started: CheckM
[2024-01-24 13:01:48,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000711245.1_ASM71124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000711245.1_ASM71124v1_genomic.fna/checkm_input GCF_000711245.1_ASM71124v1_genomic.fna/checkm_result
[2024-01-24 13:02:34,643] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:34,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,672] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:34,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:34,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000711245.1_ASM71124v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:34,673] [INFO] Task started: Blastn
[2024-01-24 13:02:34,673] [INFO] Running command: blastn -query GCF_000711245.1_ASM71124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg761b32f8-1411-496a-b3e2-473d29cb0a8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000711245.1_ASM71124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:36,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:36,026] [INFO] Selected 17 target genomes.
[2024-01-24 13:02:36,027] [INFO] Target genome list was writen to GCF_000711245.1_ASM71124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:36,051] [INFO] Task started: fastANI
[2024-01-24 13:02:36,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f8d4b43-d4fa-4673-ab18-5a7ab56b7718/GCF_000711245.1_ASM71124v1_genomic.fna.gz --refList GCF_000711245.1_ASM71124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000711245.1_ASM71124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:47,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:47,259] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:47,260] [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_000711245.1	s__Polycyclovorans algicola	100.0	1217	1217	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	82.4476	658	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	99.22	98.54	0.87	0.78	3	-
GCA_016918765.1	s__Polycyclovorans sp016918765	78.6637	346	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	78.0034	313	1217	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_002930645.1	s__Solimonas_A fluminis	77.7287	291	1217	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	77.5696	288	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.5542	246	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297005.1	s__Stagnimonas sp004297005	77.4877	252	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	99.89	99.89	0.87	0.87	2	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	77.3636	290	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	77.3063	286	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	77.2996	288	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	77.2815	247	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	76.864	190	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476065.1	s__Luteimonas_B lumbrici	76.5733	116	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782025.1	s__Azonexus sp009782025	76.284	52	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940015.1	s__Xanthomonas melonis	76.2047	102	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.1512	103	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:47,261] [INFO] GTDB search result was written to GCF_000711245.1_ASM71124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:47,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:47,266] [INFO] DFAST_QC result json was written to GCF_000711245.1_ASM71124v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:47,266] [INFO] DFAST_QC completed!
[2024-01-24 13:02:47,266] [INFO] Total running time: 0h1m28s