[2023-06-30 21:41:18,898] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:41:18,900] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:41:18,900] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference
[2023-06-30 21:41:21,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:41:21,275] [INFO] Task started: Prodigal
[2023-06-30 21:41:21,275] [INFO] Running command: gunzip -c /var/lib/cwl/stge51e13ec-6326-4063-8eb6-3e9a31dcd249/GCA_016873405.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016873405.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016873405.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:41:27,569] [INFO] Task succeeded: Prodigal
[2023-06-30 21:41:27,570] [INFO] Task started: HMMsearch
[2023-06-30 21:41:27,570] [INFO] Running command: hmmsearch --tblout GCA_016873405.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference/reference_markers.hmm GCA_016873405.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:41:27,844] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:41:27,845] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge51e13ec-6326-4063-8eb6-3e9a31dcd249/GCA_016873405.1_JGI_2017-08-21_genomic.fna.gz]
[2023-06-30 21:41:27,879] [INFO] Query marker FASTA was written to GCA_016873405.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-06-30 21:41:27,879] [INFO] Task started: Blastn
[2023-06-30 21:41:27,879] [INFO] Running command: blastn -query GCA_016873405.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference/reference_markers.fasta -out GCA_016873405.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:41:28,581] [INFO] Task succeeded: Blastn
[2023-06-30 21:41:28,586] [INFO] Selected 24 target genomes.
[2023-06-30 21:41:28,587] [INFO] Target genome list was writen to GCA_016873405.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-06-30 21:41:28,591] [INFO] Task started: fastANI
[2023-06-30 21:41:28,591] [INFO] Running command: fastANI --query /var/lib/cwl/stge51e13ec-6326-4063-8eb6-3e9a31dcd249/GCA_016873405.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016873405.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016873405.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:41:45,265] [INFO] Task succeeded: fastANI
[2023-06-30 21:41:45,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:41:45,266] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:41:45,287] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:41:45,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 21:41:45,287] [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
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.1137	74	585	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	75.0862	78	585	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.0163	107	585	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.0102	97	585	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	75.0071	80	585	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	75.0014	101	585	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	74.9764	59	585	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.9669	116	585	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.9663	98	585	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9647	80	585	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	74.9456	126	585	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	74.929	92	585	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.9282	90	585	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	74.9239	157	585	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	74.9049	151	585	95	below_threshold
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	74.8307	119	585	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	74.735	80	585	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	74.7196	85	585	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	74.716	86	585	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 21:41:45,290] [INFO] DFAST Taxonomy check result was written to GCA_016873405.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-06-30 21:41:45,290] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:41:45,291] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:41:45,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference/checkm_data
[2023-06-30 21:41:45,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:41:45,326] [INFO] Task started: CheckM
[2023-06-30 21:41:45,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016873405.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016873405.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016873405.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-06-30 21:42:09,404] [INFO] Task succeeded: CheckM
[2023-06-30 21:42:09,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.66%
Contamintation: 5.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 21:42:09,431] [INFO] ===== Completeness check finished =====
[2023-06-30 21:42:09,432] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:42:09,432] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016873405.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-06-30 21:42:09,432] [INFO] Task started: Blastn
[2023-06-30 21:42:09,433] [INFO] Running command: blastn -query GCA_016873405.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd265737-f55b-43c8-be75-2858a34f8d84/dqc_reference/reference_markers_gtdb.fasta -out GCA_016873405.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:42:10,543] [INFO] Task succeeded: Blastn
[2023-06-30 21:42:10,548] [INFO] Selected 6 target genomes.
[2023-06-30 21:42:10,548] [INFO] Target genome list was writen to GCA_016873405.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:42:10,550] [INFO] Task started: fastANI
[2023-06-30 21:42:10,550] [INFO] Running command: fastANI --query /var/lib/cwl/stge51e13ec-6326-4063-8eb6-3e9a31dcd249/GCA_016873405.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016873405.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016873405.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:42:15,138] [INFO] Task succeeded: fastANI
[2023-06-30 21:42:15,149] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:42:15,149] [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_016873405.1	s__CAINDZ01 sp016873405	100.0	573	585	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	conclusive
GCA_016712675.1	s__CAINDZ01 sp016712675	86.0864	505	585	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_016703265.1	s__CAINDZ01 sp016703265	82.8554	471	585	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	-
GCA_903859215.1	s__CAINDZ01 sp903859215	82.4172	418	585	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_903847545.1	s__CAINDZ01 sp903847545	82.3755	346	585	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	82.0854	444	585	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	-
--------------------------------------------------------------------------------
[2023-06-30 21:42:15,151] [INFO] GTDB search result was written to GCA_016873405.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-06-30 21:42:15,151] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:42:15,159] [INFO] DFAST_QC result json was written to GCA_016873405.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-06-30 21:42:15,160] [INFO] DFAST_QC completed!
[2023-06-30 21:42:15,160] [INFO] Total running time: 0h0m56s