[2023-07-01 02:37:48,829] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:37:48,831] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:37:48,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference
[2023-07-01 02:37:50,830] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:37:50,831] [INFO] Task started: Prodigal
[2023-07-01 02:37:50,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf881e3e-1970-4fda-b6d9-5c6854b561de/GCA_016708495.1_ASM1670849v1_genomic.fna.gz | prodigal -d GCA_016708495.1_ASM1670849v1_genomic.fna/cds.fna -a GCA_016708495.1_ASM1670849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:38:07,271] [INFO] Task succeeded: Prodigal
[2023-07-01 02:38:07,271] [INFO] Task started: HMMsearch
[2023-07-01 02:38:07,272] [INFO] Running command: hmmsearch --tblout GCA_016708495.1_ASM1670849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference/reference_markers.hmm GCA_016708495.1_ASM1670849v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:38:07,580] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:38:07,581] [INFO] Found 6/6 markers.
[2023-07-01 02:38:07,624] [INFO] Query marker FASTA was written to GCA_016708495.1_ASM1670849v1_genomic.fna/markers.fasta
[2023-07-01 02:38:07,624] [INFO] Task started: Blastn
[2023-07-01 02:38:07,624] [INFO] Running command: blastn -query GCA_016708495.1_ASM1670849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference/reference_markers.fasta -out GCA_016708495.1_ASM1670849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:38:08,388] [INFO] Task succeeded: Blastn
[2023-07-01 02:38:08,393] [INFO] Selected 32 target genomes.
[2023-07-01 02:38:08,393] [INFO] Target genome list was writen to GCA_016708495.1_ASM1670849v1_genomic.fna/target_genomes.txt
[2023-07-01 02:38:08,419] [INFO] Task started: fastANI
[2023-07-01 02:38:08,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf881e3e-1970-4fda-b6d9-5c6854b561de/GCA_016708495.1_ASM1670849v1_genomic.fna.gz --refList GCA_016708495.1_ASM1670849v1_genomic.fna/target_genomes.txt --output GCA_016708495.1_ASM1670849v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:38:29,466] [INFO] Task succeeded: fastANI
[2023-07-01 02:38:29,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:38:29,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:38:29,499] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:38:29,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:38:29,500] [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
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	75.3721	123	1794	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	75.3473	127	1794	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	75.3105	147	1794	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	75.3019	160	1794	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.2248	134	1794	95	below_threshold
Gemmatimonas aurantiaca	strain=T-27	GCA_000010305.1	173480	173480	type	True	75.1907	54	1794	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.1686	135	1794	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.1527	189	1794	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	75.1368	99	1794	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	75.1324	186	1794	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	75.1202	217	1794	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.1121	177	1794	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.0917	200	1794	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	75.0761	157	1794	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	75.0611	240	1794	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	75.0382	130	1794	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	75.0312	78	1794	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.0312	172	1794	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.024	174	1794	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	74.9615	209	1794	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	74.958	94	1794	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	74.9558	118	1794	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	74.919	81	1794	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	74.8853	128	1794	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	74.8758	103	1794	95	below_threshold
Cellulomonas xylanilytica	strain=NBRC 101102	GCA_007989805.1	233583	233583	type	True	74.8194	123	1794	95	below_threshold
Arthrobacter castelli	strain=DSM 16402	GCA_000430705.1	271431	271431	type	True	74.764	52	1794	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:38:29,502] [INFO] DFAST Taxonomy check result was written to GCA_016708495.1_ASM1670849v1_genomic.fna/tc_result.tsv
[2023-07-01 02:38:29,502] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:38:29,503] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:38:29,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference/checkm_data
[2023-07-01 02:38:29,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:38:29,556] [INFO] Task started: CheckM
[2023-07-01 02:38:29,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708495.1_ASM1670849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708495.1_ASM1670849v1_genomic.fna/checkm_input GCA_016708495.1_ASM1670849v1_genomic.fna/checkm_result
[2023-07-01 02:39:34,232] [INFO] Task succeeded: CheckM
[2023-07-01 02:39:34,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:39:34,259] [INFO] ===== Completeness check finished =====
[2023-07-01 02:39:34,260] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:39:34,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708495.1_ASM1670849v1_genomic.fna/markers.fasta)
[2023-07-01 02:39:34,261] [INFO] Task started: Blastn
[2023-07-01 02:39:34,261] [INFO] Running command: blastn -query GCA_016708495.1_ASM1670849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36a0e8bd-9212-4915-a3c5-fdad12bb866d/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708495.1_ASM1670849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:39:35,434] [INFO] Task succeeded: Blastn
[2023-07-01 02:39:35,439] [INFO] Selected 6 target genomes.
[2023-07-01 02:39:35,439] [INFO] Target genome list was writen to GCA_016708495.1_ASM1670849v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:39:35,441] [INFO] Task started: fastANI
[2023-07-01 02:39:35,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf881e3e-1970-4fda-b6d9-5c6854b561de/GCA_016708495.1_ASM1670849v1_genomic.fna.gz --refList GCA_016708495.1_ASM1670849v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708495.1_ASM1670849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:39:41,950] [INFO] Task succeeded: fastANI
[2023-07-01 02:39:41,962] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:39:41,962] [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_016703265.1	s__CAINDZ01 sp016703265	96.1243	1379	1794	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	96.41	95.95	0.89	0.87	7	conclusive
GCA_016712675.1	s__CAINDZ01 sp016712675	83.7384	1091	1794	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847545.1	s__CAINDZ01 sp903847545	83.5629	650	1794	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	98.70	98.54	0.79	0.77	4	-
GCA_903912525.1	s__CAINDZ01 sp903912525	83.2908	970	1794	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859215.1	s__CAINDZ01 sp903859215	83.2429	908	1794	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	99.58	99.58	0.89	0.89	2	-
GCA_016873405.1	s__CAINDZ01 sp016873405	82.9793	488	1794	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:39:41,965] [INFO] GTDB search result was written to GCA_016708495.1_ASM1670849v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:39:41,965] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:39:41,969] [INFO] DFAST_QC result json was written to GCA_016708495.1_ASM1670849v1_genomic.fna/dqc_result.json
[2023-07-01 02:39:41,970] [INFO] DFAST_QC completed!
[2023-07-01 02:39:41,970] [INFO] Total running time: 0h1m53s