[2023-06-27 14:43:38,111] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:43:38,114] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:43:38,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference
[2023-06-27 14:43:39,424] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:43:39,425] [INFO] Task started: Prodigal
[2023-06-27 14:43:39,425] [INFO] Running command: gunzip -c /var/lib/cwl/stgb961330f-ed4b-4eb9-ac63-9748b392b674/GCA_026710005.1_ASM2671000v1_genomic.fna.gz | prodigal -d GCA_026710005.1_ASM2671000v1_genomic.fna/cds.fna -a GCA_026710005.1_ASM2671000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:43:46,316] [INFO] Task succeeded: Prodigal
[2023-06-27 14:43:46,316] [INFO] Task started: HMMsearch
[2023-06-27 14:43:46,316] [INFO] Running command: hmmsearch --tblout GCA_026710005.1_ASM2671000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference/reference_markers.hmm GCA_026710005.1_ASM2671000v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:43:46,553] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:43:46,555] [INFO] Found 6/6 markers.
[2023-06-27 14:43:46,580] [INFO] Query marker FASTA was written to GCA_026710005.1_ASM2671000v1_genomic.fna/markers.fasta
[2023-06-27 14:43:46,581] [INFO] Task started: Blastn
[2023-06-27 14:43:46,581] [INFO] Running command: blastn -query GCA_026710005.1_ASM2671000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference/reference_markers.fasta -out GCA_026710005.1_ASM2671000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:43:47,305] [INFO] Task succeeded: Blastn
[2023-06-27 14:43:47,310] [INFO] Selected 32 target genomes.
[2023-06-27 14:43:47,311] [INFO] Target genome list was writen to GCA_026710005.1_ASM2671000v1_genomic.fna/target_genomes.txt
[2023-06-27 14:43:47,330] [INFO] Task started: fastANI
[2023-06-27 14:43:47,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgb961330f-ed4b-4eb9-ac63-9748b392b674/GCA_026710005.1_ASM2671000v1_genomic.fna.gz --refList GCA_026710005.1_ASM2671000v1_genomic.fna/target_genomes.txt --output GCA_026710005.1_ASM2671000v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:44:06,370] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:06,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:44:06,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:44:06,394] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:44:06,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:44:06,395] [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
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.6547	83	711	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.6295	89	711	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.4445	78	711	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.3815	91	711	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.3785	104	711	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.375	89	711	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.2438	78	711	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	76.201	87	711	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.1785	117	711	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.1297	84	711	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.1059	62	711	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.0897	74	711	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	76.0474	69	711	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	75.993	82	711	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.9268	92	711	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	75.8323	82	711	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.8248	78	711	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	75.6949	71	711	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	75.6534	55	711	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.6209	67	711	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	75.5729	74	711	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.4567	73	711	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	75.3452	62	711	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	75.3452	62	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:44:06,397] [INFO] DFAST Taxonomy check result was written to GCA_026710005.1_ASM2671000v1_genomic.fna/tc_result.tsv
[2023-06-27 14:44:06,398] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:44:06,398] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:44:06,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference/checkm_data
[2023-06-27 14:44:06,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:44:06,435] [INFO] Task started: CheckM
[2023-06-27 14:44:06,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026710005.1_ASM2671000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026710005.1_ASM2671000v1_genomic.fna/checkm_input GCA_026710005.1_ASM2671000v1_genomic.fna/checkm_result
[2023-06-27 14:44:31,599] [INFO] Task succeeded: CheckM
[2023-06-27 14:44:31,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:44:31,626] [INFO] ===== Completeness check finished =====
[2023-06-27 14:44:31,627] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:44:31,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026710005.1_ASM2671000v1_genomic.fna/markers.fasta)
[2023-06-27 14:44:31,627] [INFO] Task started: Blastn
[2023-06-27 14:44:31,628] [INFO] Running command: blastn -query GCA_026710005.1_ASM2671000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3780c56a-06a8-4dcb-95e4-ecbfd6175789/dqc_reference/reference_markers_gtdb.fasta -out GCA_026710005.1_ASM2671000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:32,707] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:32,714] [INFO] Selected 27 target genomes.
[2023-06-27 14:44:32,714] [INFO] Target genome list was writen to GCA_026710005.1_ASM2671000v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:44:32,756] [INFO] Task started: fastANI
[2023-06-27 14:44:32,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgb961330f-ed4b-4eb9-ac63-9748b392b674/GCA_026710005.1_ASM2671000v1_genomic.fna.gz --refList GCA_026710005.1_ASM2671000v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026710005.1_ASM2671000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:44:47,717] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:47,739] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 14:44:47,739] [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_009844085.1	s__UBA9145 sp009844085	80.2926	445	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.17	97.62	0.91	0.85	13	-
GCA_007571115.1	s__UBA9145 sp007571115	78.8276	234	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.87	98.87	0.74	0.74	2	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	76.582	99	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.4949	98	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	76.3673	96	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	76.3565	76	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_003202205.1	s__Halomonas sp003202205	76.3215	89	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.3076	105	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	76.2127	71	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCA_004551485.1	s__Halomonas azerbaijanica	76.1814	91	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	76.1396	73	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764025.1	s__Pseudohaliea rubra	76.0794	63	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Pseudohaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380335.1	s__Azotobacter vinelandii	75.9731	93	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	75.907	72	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.7878	90	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_900112865.1	s__Dyella marensis	75.7661	68	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCA_011389995.1	s__JAABTG01 sp011389995	75.6826	52	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAABTG01;f__JAABTG01;g__JAABTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093185.1	s__Pseudoxanthomonas jiangsuensis	75.6597	73	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709695.1	s__QUBU01 sp015709695	75.6474	54	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	75.5729	74	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	75.4567	73	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694905.1	s__SLTB01 sp007694905	75.3259	58	711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 14:44:47,741] [INFO] GTDB search result was written to GCA_026710005.1_ASM2671000v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:44:47,742] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:44:47,748] [INFO] DFAST_QC result json was written to GCA_026710005.1_ASM2671000v1_genomic.fna/dqc_result.json
[2023-06-27 14:44:47,749] [INFO] DFAST_QC completed!
[2023-06-27 14:44:47,749] [INFO] Total running time: 0h1m10s