[2023-07-01 05:18:02,329] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:18:02,367] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:18:02,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference
[2023-07-01 05:18:03,543] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:18:03,544] [INFO] Task started: Prodigal
[2023-07-01 05:18:03,545] [INFO] Running command: gunzip -c /var/lib/cwl/stg30222579-b52d-4a8a-a4b4-43589d74477c/GCA_024234635.1_ASM2423463v1_genomic.fna.gz | prodigal -d GCA_024234635.1_ASM2423463v1_genomic.fna/cds.fna -a GCA_024234635.1_ASM2423463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:18:18,411] [INFO] Task succeeded: Prodigal
[2023-07-01 05:18:18,411] [INFO] Task started: HMMsearch
[2023-07-01 05:18:18,411] [INFO] Running command: hmmsearch --tblout GCA_024234635.1_ASM2423463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference/reference_markers.hmm GCA_024234635.1_ASM2423463v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:18:18,644] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:18:18,645] [INFO] Found 6/6 markers.
[2023-07-01 05:18:18,684] [INFO] Query marker FASTA was written to GCA_024234635.1_ASM2423463v1_genomic.fna/markers.fasta
[2023-07-01 05:18:18,684] [INFO] Task started: Blastn
[2023-07-01 05:18:18,684] [INFO] Running command: blastn -query GCA_024234635.1_ASM2423463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference/reference_markers.fasta -out GCA_024234635.1_ASM2423463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:18:19,480] [INFO] Task succeeded: Blastn
[2023-07-01 05:18:19,483] [INFO] Selected 31 target genomes.
[2023-07-01 05:18:19,483] [INFO] Target genome list was writen to GCA_024234635.1_ASM2423463v1_genomic.fna/target_genomes.txt
[2023-07-01 05:18:19,484] [INFO] Task started: fastANI
[2023-07-01 05:18:19,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg30222579-b52d-4a8a-a4b4-43589d74477c/GCA_024234635.1_ASM2423463v1_genomic.fna.gz --refList GCA_024234635.1_ASM2423463v1_genomic.fna/target_genomes.txt --output GCA_024234635.1_ASM2423463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:18:37,846] [INFO] Task succeeded: fastANI
[2023-07-01 05:18:37,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:18:37,847] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:18:37,862] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:18:37,862] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 05:18:37,863] [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
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.0296	82	1494	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.7299	59	1494	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	75.713	72	1494	95	below_threshold
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	75.71	51	1494	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	75.6966	62	1494	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	75.6835	50	1494	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.5827	120	1494	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.55	120	1494	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.5441	97	1494	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	75.5135	50	1494	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	75.5026	75	1494	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	75.491	100	1494	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	75.4854	50	1494	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	75.4618	62	1494	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	75.3359	60	1494	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	75.3302	57	1494	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	75.2094	58	1494	95	below_threshold
Kushneria sinocarnis	strain=DSM 23229	GCA_003633775.1	595502	595502	type	True	75.2049	50	1494	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.2035	53	1494	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	75.1239	55	1494	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	75.0534	54	1494	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 05:18:37,876] [INFO] DFAST Taxonomy check result was written to GCA_024234635.1_ASM2423463v1_genomic.fna/tc_result.tsv
[2023-07-01 05:18:37,877] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:18:37,877] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:18:37,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference/checkm_data
[2023-07-01 05:18:37,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:18:37,919] [INFO] Task started: CheckM
[2023-07-01 05:18:37,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024234635.1_ASM2423463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024234635.1_ASM2423463v1_genomic.fna/checkm_input GCA_024234635.1_ASM2423463v1_genomic.fna/checkm_result
[2023-07-01 05:19:25,310] [INFO] Task succeeded: CheckM
[2023-07-01 05:19:25,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:19:25,340] [INFO] ===== Completeness check finished =====
[2023-07-01 05:19:25,341] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:19:25,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024234635.1_ASM2423463v1_genomic.fna/markers.fasta)
[2023-07-01 05:19:25,341] [INFO] Task started: Blastn
[2023-07-01 05:19:25,341] [INFO] Running command: blastn -query GCA_024234635.1_ASM2423463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155e01be-3dcf-4a81-a485-33ebbd28d6f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_024234635.1_ASM2423463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:19:26,745] [INFO] Task succeeded: Blastn
[2023-07-01 05:19:26,749] [INFO] Selected 32 target genomes.
[2023-07-01 05:19:26,749] [INFO] Target genome list was writen to GCA_024234635.1_ASM2423463v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:19:26,752] [INFO] Task started: fastANI
[2023-07-01 05:19:26,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg30222579-b52d-4a8a-a4b4-43589d74477c/GCA_024234635.1_ASM2423463v1_genomic.fna.gz --refList GCA_024234635.1_ASM2423463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024234635.1_ASM2423463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:19:45,417] [INFO] Task succeeded: fastANI
[2023-07-01 05:19:45,432] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 05:19:45,433] [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_016874135.1	s__SYFY01 sp016874135	76.6973	199	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SYFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480525.1	s__UBA7803 sp002480525	76.4368	207	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	-
GCA_003248125.1	s__SZUA-521 sp003248125	76.3113	61	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-521	95.0	99.60	99.60	0.84	0.84	2	-
GCF_015712065.1	s__Pseudomonas_E chengduensis_A	76.1083	66	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7107	97.25	97.17	0.91	0.89	9	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	76.091	68	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCA_009843635.1	s__UBA2168 sp009843635	76.017	107	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2168	95.0	97.76	96.95	0.89	0.86	7	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	75.9659	73	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694905.1	s__SLTB01 sp007694905	75.8525	90	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089885.1	s__XN24 sp011089885	75.8396	60	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	75.6966	62	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCA_009837725.1	s__VXYL01 sp009837725	75.6847	71	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__VXYL01	95.0	97.81	97.81	0.84	0.84	2	-
GCA_003476445.1	s__UBA7803 sp003476445	75.619	70	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131295.1	s__SLTB01 sp007131295	75.5645	63	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	99.75	99.70	0.93	0.92	5	-
GCF_900187975.1	s__Pseudomonas delhiensis	75.5574	119	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_001270295.1	s__Achromobacter sp001270295	75.461	67	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	75.3111	94	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_001534745.1	s__Pseudomonas_E monteilii_A	75.3046	66	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.81	97.29	0.91	0.89	7	-
GCF_018599185.1	s__Rhodanobacter sp018599185	75.2157	57	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000230695.2	s__Rhodanobacter denitrificans	75.2094	58	1494	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.49	98.47	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2023-07-01 05:19:45,435] [INFO] GTDB search result was written to GCA_024234635.1_ASM2423463v1_genomic.fna/result_gtdb.tsv
[2023-07-01 05:19:45,435] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:19:45,444] [INFO] DFAST_QC result json was written to GCA_024234635.1_ASM2423463v1_genomic.fna/dqc_result.json
[2023-07-01 05:19:45,444] [INFO] DFAST_QC completed!
[2023-07-01 05:19:45,444] [INFO] Total running time: 0h1m43s