[2023-06-27 01:35:30,781] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:35:30,784] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:35:30,784] [INFO] DQC Reference Directory: /var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference
[2023-06-27 01:35:32,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:35:32,166] [INFO] Task started: Prodigal
[2023-06-27 01:35:32,166] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0e42cea-19f6-4d19-839b-5958cecf1a65/GCA_026708055.1_ASM2670805v1_genomic.fna.gz | prodigal -d GCA_026708055.1_ASM2670805v1_genomic.fna/cds.fna -a GCA_026708055.1_ASM2670805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:35:44,125] [INFO] Task succeeded: Prodigal
[2023-06-27 01:35:44,126] [INFO] Task started: HMMsearch
[2023-06-27 01:35:44,126] [INFO] Running command: hmmsearch --tblout GCA_026708055.1_ASM2670805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference/reference_markers.hmm GCA_026708055.1_ASM2670805v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:35:44,505] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:35:44,506] [INFO] Found 6/6 markers.
[2023-06-27 01:35:44,545] [INFO] Query marker FASTA was written to GCA_026708055.1_ASM2670805v1_genomic.fna/markers.fasta
[2023-06-27 01:35:44,545] [INFO] Task started: Blastn
[2023-06-27 01:35:44,546] [INFO] Running command: blastn -query GCA_026708055.1_ASM2670805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference/reference_markers.fasta -out GCA_026708055.1_ASM2670805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:35:45,329] [INFO] Task succeeded: Blastn
[2023-06-27 01:35:45,333] [INFO] Selected 28 target genomes.
[2023-06-27 01:35:45,333] [INFO] Target genome list was writen to GCA_026708055.1_ASM2670805v1_genomic.fna/target_genomes.txt
[2023-06-27 01:35:45,338] [INFO] Task started: fastANI
[2023-06-27 01:35:45,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0e42cea-19f6-4d19-839b-5958cecf1a65/GCA_026708055.1_ASM2670805v1_genomic.fna.gz --refList GCA_026708055.1_ASM2670805v1_genomic.fna/target_genomes.txt --output GCA_026708055.1_ASM2670805v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 01:36:09,015] [INFO] Task succeeded: fastANI
[2023-06-27 01:36:09,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 01:36:09,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 01:36:09,045] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 01:36:09,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 01:36:09,046] [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	76.4841	200	1264	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.4471	162	1264	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.4415	199	1264	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.8011	199	1264	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.7302	85	1264	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6944	151	1264	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.6549	136	1264	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	75.4282	85	1264	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	75.405	171	1264	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	75.3415	107	1264	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	75.2619	89	1264	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	75.2479	156	1264	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	75.1419	211	1264	95	below_threshold
Pseudonocardia endophytica	strain=DSM 44969	GCA_004339565.1	401976	401976	type	True	75.0837	184	1264	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	75.0531	80	1264	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	75.0173	154	1264	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	74.988	188	1264	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	74.9635	149	1264	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	74.9625	90	1264	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	74.9351	88	1264	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.9333	110	1264	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	74.9313	89	1264	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	74.9043	196	1264	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	74.6866	111	1264	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 01:36:09,048] [INFO] DFAST Taxonomy check result was written to GCA_026708055.1_ASM2670805v1_genomic.fna/tc_result.tsv
[2023-06-27 01:36:09,049] [INFO] ===== Taxonomy check completed =====
[2023-06-27 01:36:09,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:36:09,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference/checkm_data
[2023-06-27 01:36:09,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:36:09,096] [INFO] Task started: CheckM
[2023-06-27 01:36:09,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708055.1_ASM2670805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708055.1_ASM2670805v1_genomic.fna/checkm_input GCA_026708055.1_ASM2670805v1_genomic.fna/checkm_result
[2023-06-27 01:36:49,651] [INFO] Task succeeded: CheckM
[2023-06-27 01:36:49,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:36:49,675] [INFO] ===== Completeness check finished =====
[2023-06-27 01:36:49,675] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:36:49,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708055.1_ASM2670805v1_genomic.fna/markers.fasta)
[2023-06-27 01:36:49,676] [INFO] Task started: Blastn
[2023-06-27 01:36:49,676] [INFO] Running command: blastn -query GCA_026708055.1_ASM2670805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea62f973-8cd3-4b52-a298-db8943979c7b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708055.1_ASM2670805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:36:50,835] [INFO] Task succeeded: Blastn
[2023-06-27 01:36:50,839] [INFO] Selected 20 target genomes.
[2023-06-27 01:36:50,839] [INFO] Target genome list was writen to GCA_026708055.1_ASM2670805v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:36:50,847] [INFO] Task started: fastANI
[2023-06-27 01:36:50,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0e42cea-19f6-4d19-839b-5958cecf1a65/GCA_026708055.1_ASM2670805v1_genomic.fna.gz --refList GCA_026708055.1_ASM2670805v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708055.1_ASM2670805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:37:02,093] [INFO] Task succeeded: fastANI
[2023-06-27 01:37:02,115] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:37:02,116] [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_009835395.1	s__VXNF01 sp009835395	89.714	822	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	99.94	99.92	0.97	0.97	3	-
GCA_009840735.1	s__VXNF01 sp009840735	84.6103	677	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Bin134;g__VXNF01	95.0	98.98	98.92	0.89	0.88	3	-
GCA_016845305.1	s__UBA9410 sp016845305	77.5438	211	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837445.1	s__VYCW01 sp009837445	77.3633	272	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.43	98.40	0.97	0.95	9	-
GCA_009843915.1	s__VYCW01 sp009843915	77.2959	227	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	97.45	96.57	0.82	0.78	5	-
GCA_002727895.1	s__UBA9410 sp002727895	76.9182	124	1264	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_014381945.1	s__S20-B6 sp014381945	76.902	150	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	76.5784	211	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051915.1	s__DRKF01 sp011051915	76.5739	112	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__DRKF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	76.3531	226	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	76.2955	133	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.1999	168	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_902805665.1	s__CADCTB01 sp902805665	76.1893	125	1264	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_016185275.1	s__JACPNX01 sp016185275	76.1422	165	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.1173	111	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	75.7437	164	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.4613	150	1264	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180685.1	s__Nocardioides pelophilus	75.3204	107	1264	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793875.1	s__SSA4 sp016793875	74.9812	59	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097155.1	s__Glacieibacterium frigidum	74.8712	64	1264	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 01:37:02,118] [INFO] GTDB search result was written to GCA_026708055.1_ASM2670805v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:37:02,119] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:37:02,128] [INFO] DFAST_QC result json was written to GCA_026708055.1_ASM2670805v1_genomic.fna/dqc_result.json
[2023-06-27 01:37:02,128] [INFO] DFAST_QC completed!
[2023-06-27 01:37:02,129] [INFO] Total running time: 0h1m31s