[2023-06-17 05:04:41,103] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:04:41,107] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:04:41,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference
[2023-06-17 05:04:42,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:04:42,522] [INFO] Task started: Prodigal
[2023-06-17 05:04:42,522] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f71dc75-9a27-4259-ac0d-fc8f569e76ea/GCA_009836375.1_ASM983637v1_genomic.fna.gz | prodigal -d GCA_009836375.1_ASM983637v1_genomic.fna/cds.fna -a GCA_009836375.1_ASM983637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:04:54,210] [INFO] Task succeeded: Prodigal
[2023-06-17 05:04:54,210] [INFO] Task started: HMMsearch
[2023-06-17 05:04:54,210] [INFO] Running command: hmmsearch --tblout GCA_009836375.1_ASM983637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference/reference_markers.hmm GCA_009836375.1_ASM983637v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:04:54,469] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:04:54,470] [INFO] Found 6/6 markers.
[2023-06-17 05:04:54,511] [INFO] Query marker FASTA was written to GCA_009836375.1_ASM983637v1_genomic.fna/markers.fasta
[2023-06-17 05:04:54,511] [INFO] Task started: Blastn
[2023-06-17 05:04:54,512] [INFO] Running command: blastn -query GCA_009836375.1_ASM983637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference/reference_markers.fasta -out GCA_009836375.1_ASM983637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:04:55,310] [INFO] Task succeeded: Blastn
[2023-06-17 05:04:55,315] [INFO] Selected 27 target genomes.
[2023-06-17 05:04:55,315] [INFO] Target genome list was writen to GCA_009836375.1_ASM983637v1_genomic.fna/target_genomes.txt
[2023-06-17 05:04:55,323] [INFO] Task started: fastANI
[2023-06-17 05:04:55,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f71dc75-9a27-4259-ac0d-fc8f569e76ea/GCA_009836375.1_ASM983637v1_genomic.fna.gz --refList GCA_009836375.1_ASM983637v1_genomic.fna/target_genomes.txt --output GCA_009836375.1_ASM983637v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:05:13,832] [INFO] Task succeeded: fastANI
[2023-06-17 05:05:13,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:05:13,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:05:13,847] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:05:13,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 05:05:13,848] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.8554	154	1168	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.7418	153	1168	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.2795	152	1168	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.2741	97	1168	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.0475	170	1168	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	75.8191	60	1168	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	75.8126	57	1168	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	75.5531	62	1168	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	75.5505	86	1168	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	75.509	90	1168	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.449	77	1168	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	75.4383	76	1168	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	75.3756	56	1168	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	75.3718	95	1168	95	below_threshold
Kineosporia corallincola	strain=J2-2	GCA_018499875.1	2835133	2835133	type	True	75.3504	115	1168	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	75.1397	65	1168	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	74.9964	57	1168	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 05:05:13,866] [INFO] DFAST Taxonomy check result was written to GCA_009836375.1_ASM983637v1_genomic.fna/tc_result.tsv
[2023-06-17 05:05:13,867] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:05:13,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:05:13,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference/checkm_data
[2023-06-17 05:05:13,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:05:13,910] [INFO] Task started: CheckM
[2023-06-17 05:05:13,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009836375.1_ASM983637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009836375.1_ASM983637v1_genomic.fna/checkm_input GCA_009836375.1_ASM983637v1_genomic.fna/checkm_result
[2023-06-17 05:05:54,411] [INFO] Task succeeded: CheckM
[2023-06-17 05:05:54,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 05:05:54,438] [INFO] ===== Completeness check finished =====
[2023-06-17 05:05:54,439] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:05:54,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009836375.1_ASM983637v1_genomic.fna/markers.fasta)
[2023-06-17 05:05:54,439] [INFO] Task started: Blastn
[2023-06-17 05:05:54,440] [INFO] Running command: blastn -query GCA_009836375.1_ASM983637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11b41431-3e1c-4a07-ac37-e3e47388ba41/dqc_reference/reference_markers_gtdb.fasta -out GCA_009836375.1_ASM983637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:05:55,521] [INFO] Task succeeded: Blastn
[2023-06-17 05:05:55,527] [INFO] Selected 22 target genomes.
[2023-06-17 05:05:55,527] [INFO] Target genome list was writen to GCA_009836375.1_ASM983637v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:05:55,544] [INFO] Task started: fastANI
[2023-06-17 05:05:55,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f71dc75-9a27-4259-ac0d-fc8f569e76ea/GCA_009836375.1_ASM983637v1_genomic.fna.gz --refList GCA_009836375.1_ASM983637v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009836375.1_ASM983637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:06:07,383] [INFO] Task succeeded: fastANI
[2023-06-17 05:06:07,402] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 05:06:07,402] [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_009843525.1	s__WTFX01 sp009843525	97.4978	978	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	98.04	97.52	0.89	0.86	18	conclusive
GCA_011523825.1	s__WTFX01 sp011523825	89.3056	871	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__WTFX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837445.1	s__VYCW01 sp009837445	77.3973	209	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.43	98.40	0.97	0.95	9	-
GCA_002727895.1	s__UBA9410 sp002727895	77.153	83	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_011051915.1	s__DRKF01 sp011051915	77.0473	110	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__DRKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	76.9924	97	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.7285	154	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.667	104	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882825.1	s__F1-20-MAGs160 sp018882825	76.5479	91	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	76.4464	70	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.4353	120	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_016870275.1	s__SXMI01 sp016870275	76.398	73	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888395.1	s__AC-25 sp005888395	76.3524	91	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247975.1	s__JAFBAD01 sp019247975	76.2493	100	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAFBAD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377505.1	s__WHTX01 sp009377505	76.2438	166	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__WHTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	76.1298	100	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.9822	94	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888295.1	s__AC-9 sp005888295	75.9637	93	1168	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733795.1	s__Pseudactinotalea caeni	75.5139	86	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Beutenbergiaceae;g__Pseudactinotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611035.1	s__Cryobacterium soli	75.3531	59	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 05:06:07,404] [INFO] GTDB search result was written to GCA_009836375.1_ASM983637v1_genomic.fna/result_gtdb.tsv
[2023-06-17 05:06:07,405] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:06:07,409] [INFO] DFAST_QC result json was written to GCA_009836375.1_ASM983637v1_genomic.fna/dqc_result.json
[2023-06-17 05:06:07,410] [INFO] DFAST_QC completed!
[2023-06-17 05:06:07,410] [INFO] Total running time: 0h1m26s