[2023-06-29 13:53:42,572] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:53:42,575] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:53:42,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference
[2023-06-29 13:53:43,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:53:43,946] [INFO] Task started: Prodigal
[2023-06-29 13:53:43,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d3926fe-bc2f-4234-b299-e68b0fba7945/GCA_021787365.1_ASM2178736v1_genomic.fna.gz | prodigal -d GCA_021787365.1_ASM2178736v1_genomic.fna/cds.fna -a GCA_021787365.1_ASM2178736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:53:56,741] [INFO] Task succeeded: Prodigal
[2023-06-29 13:53:56,741] [INFO] Task started: HMMsearch
[2023-06-29 13:53:56,742] [INFO] Running command: hmmsearch --tblout GCA_021787365.1_ASM2178736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference/reference_markers.hmm GCA_021787365.1_ASM2178736v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:53:57,013] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:53:57,015] [INFO] Found 6/6 markers.
[2023-06-29 13:53:57,058] [INFO] Query marker FASTA was written to GCA_021787365.1_ASM2178736v1_genomic.fna/markers.fasta
[2023-06-29 13:53:57,058] [INFO] Task started: Blastn
[2023-06-29 13:53:57,059] [INFO] Running command: blastn -query GCA_021787365.1_ASM2178736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference/reference_markers.fasta -out GCA_021787365.1_ASM2178736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:53:57,713] [INFO] Task succeeded: Blastn
[2023-06-29 13:53:57,718] [INFO] Selected 23 target genomes.
[2023-06-29 13:53:57,718] [INFO] Target genome list was writen to GCA_021787365.1_ASM2178736v1_genomic.fna/target_genomes.txt
[2023-06-29 13:53:57,723] [INFO] Task started: fastANI
[2023-06-29 13:53:57,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3926fe-bc2f-4234-b299-e68b0fba7945/GCA_021787365.1_ASM2178736v1_genomic.fna.gz --refList GCA_021787365.1_ASM2178736v1_genomic.fna/target_genomes.txt --output GCA_021787365.1_ASM2178736v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:54:14,518] [INFO] Task succeeded: fastANI
[2023-06-29 13:54:14,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:54:14,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:54:14,531] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:54:14,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:54:14,531] [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	75.9633	111	1446	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.7762	120	1446	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.4597	118	1446	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	75.285	107	1446	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	75.1359	110	1446	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	75.1219	113	1446	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	75.1021	96	1446	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.0654	65	1446	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	75.0598	107	1446	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	75.0566	102	1446	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.0157	94	1446	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	74.9938	107	1446	95	below_threshold
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	74.8785	61	1446	95	below_threshold
Variovorax gossypii	strain=DSM 100435	GCA_003965815.1	1679495	1679495	type	True	74.6718	65	1446	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	74.5887	66	1446	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:54:14,533] [INFO] DFAST Taxonomy check result was written to GCA_021787365.1_ASM2178736v1_genomic.fna/tc_result.tsv
[2023-06-29 13:54:14,534] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:54:14,534] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:54:14,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference/checkm_data
[2023-06-29 13:54:14,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:54:14,578] [INFO] Task started: CheckM
[2023-06-29 13:54:14,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021787365.1_ASM2178736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021787365.1_ASM2178736v1_genomic.fna/checkm_input GCA_021787365.1_ASM2178736v1_genomic.fna/checkm_result
[2023-06-29 13:54:52,363] [INFO] Task succeeded: CheckM
[2023-06-29 13:54:52,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:54:52,388] [INFO] ===== Completeness check finished =====
[2023-06-29 13:54:52,388] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:54:52,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021787365.1_ASM2178736v1_genomic.fna/markers.fasta)
[2023-06-29 13:54:52,389] [INFO] Task started: Blastn
[2023-06-29 13:54:52,389] [INFO] Running command: blastn -query GCA_021787365.1_ASM2178736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc37b5fd2-d51c-4dcd-9fc3-31059b44b075/dqc_reference/reference_markers_gtdb.fasta -out GCA_021787365.1_ASM2178736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:54:53,304] [INFO] Task succeeded: Blastn
[2023-06-29 13:54:53,309] [INFO] Selected 29 target genomes.
[2023-06-29 13:54:53,310] [INFO] Target genome list was writen to GCA_021787365.1_ASM2178736v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:54:53,324] [INFO] Task started: fastANI
[2023-06-29 13:54:53,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3926fe-bc2f-4234-b299-e68b0fba7945/GCA_021787365.1_ASM2178736v1_genomic.fna.gz --refList GCA_021787365.1_ASM2178736v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021787365.1_ASM2178736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:55:09,556] [INFO] Task succeeded: fastANI
[2023-06-29 13:55:09,579] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:55:09,579] [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_003166025.1	s__Fen-671 sp003166025	76.9096	266	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__Fen-671	95.0	99.76	99.70	0.93	0.92	4	-
GCA_005888295.1	s__AC-9 sp005888295	76.4927	97	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002861595.1	s__GCA-2861595 sp002861595	76.2832	101	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__GCA-2861595;g__GCA-2861595	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816725.1	s__JACDEA01 sp013816725	75.9867	59	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDEA01;g__JACDEA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241495.1	s__JAFAWZ01 sp019241495	75.9585	86	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__JAFAWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	75.9094	147	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453695.1	s__UBA8190 sp003453695	75.9061	89	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__UBA8190	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805665.1	s__CADCTB01 sp902805665	75.8916	94	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADCTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003156795.1	s__PALSA-688 sp003156795	75.8652	75	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__PALSA-688	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136185.1	s__Palsa-601 sp003136185	75.8598	65	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bog-793;g__Palsa-601	95.0	99.68	99.63	0.86	0.84	3	-
GCA_016716005.1	s__JADJXE01 sp016716005	75.8223	142	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	75.7762	120	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.7528	156	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244985.1	s__CADDZP01 sp019244985	75.5055	63	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADDZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151955.1	s__PALSA-743 sp003151955	75.4922	108	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__PALSA-743	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140175.1	s__PALSA-555 sp003140175	75.4204	78	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__PALSA-555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377505.1	s__WHTX01 sp009377505	75.3661	147	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__WHTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	75.3608	102	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	75.1218	65	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	75.0654	65	1446	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655445.1	s__Diaminobutyricimonas sp015655445	74.7511	56	1446	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002870125.1	s__Paraburkholderia sp002870125	74.6564	56	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900496975.1	s__Achromobacter veterisilvae	74.5887	66	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:55:09,581] [INFO] GTDB search result was written to GCA_021787365.1_ASM2178736v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:55:09,582] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:55:09,586] [INFO] DFAST_QC result json was written to GCA_021787365.1_ASM2178736v1_genomic.fna/dqc_result.json
[2023-06-29 13:55:09,586] [INFO] DFAST_QC completed!
[2023-06-29 13:55:09,587] [INFO] Total running time: 0h1m27s