[2023-06-26 21:36:26,147] [INFO] DFAST_QC pipeline started.
[2023-06-26 21:36:26,149] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 21:36:26,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference
[2023-06-26 21:36:27,449] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 21:36:27,450] [INFO] Task started: Prodigal
[2023-06-26 21:36:27,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg211c170a-65f6-4f7f-916d-fd5e19c4da1b/GCA_026398715.1_ASM2639871v1_genomic.fna.gz | prodigal -d GCA_026398715.1_ASM2639871v1_genomic.fna/cds.fna -a GCA_026398715.1_ASM2639871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 21:36:34,899] [INFO] Task succeeded: Prodigal
[2023-06-26 21:36:34,900] [INFO] Task started: HMMsearch
[2023-06-26 21:36:34,900] [INFO] Running command: hmmsearch --tblout GCA_026398715.1_ASM2639871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference/reference_markers.hmm GCA_026398715.1_ASM2639871v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 21:36:35,096] [INFO] Task succeeded: HMMsearch
[2023-06-26 21:36:35,097] [INFO] Found 6/6 markers.
[2023-06-26 21:36:35,121] [INFO] Query marker FASTA was written to GCA_026398715.1_ASM2639871v1_genomic.fna/markers.fasta
[2023-06-26 21:36:35,121] [INFO] Task started: Blastn
[2023-06-26 21:36:35,121] [INFO] Running command: blastn -query GCA_026398715.1_ASM2639871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference/reference_markers.fasta -out GCA_026398715.1_ASM2639871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:36:35,902] [INFO] Task succeeded: Blastn
[2023-06-26 21:36:35,905] [INFO] Selected 20 target genomes.
[2023-06-26 21:36:35,905] [INFO] Target genome list was writen to GCA_026398715.1_ASM2639871v1_genomic.fna/target_genomes.txt
[2023-06-26 21:36:35,906] [INFO] Task started: fastANI
[2023-06-26 21:36:35,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg211c170a-65f6-4f7f-916d-fd5e19c4da1b/GCA_026398715.1_ASM2639871v1_genomic.fna.gz --refList GCA_026398715.1_ASM2639871v1_genomic.fna/target_genomes.txt --output GCA_026398715.1_ASM2639871v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 21:36:47,586] [INFO] Task succeeded: fastANI
[2023-06-26 21:36:47,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 21:36:47,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 21:36:47,599] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 21:36:47,599] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 21:36:47,600] [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
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	80.0647	416	807	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	80.0122	417	807	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	79.9381	380	807	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	79.8746	396	807	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	79.8407	368	807	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	79.7602	398	807	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	79.598	361	807	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	79.5591	362	807	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	78.4302	293	807	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	78.4227	273	807	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	78.3716	294	807	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	78.2811	260	807	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	78.2678	319	807	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	78.2492	308	807	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	78.2193	305	807	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	78.1978	284	807	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	78.1846	256	807	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	78.1834	261	807	95	below_threshold
Stenotrophomonas rhizophila	strain=DSM14405	GCA_000661955.1	216778	216778	suspected-type	True	78.0067	243	807	95	below_threshold
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	77.7036	167	807	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 21:36:47,601] [INFO] DFAST Taxonomy check result was written to GCA_026398715.1_ASM2639871v1_genomic.fna/tc_result.tsv
[2023-06-26 21:36:47,601] [INFO] ===== Taxonomy check completed =====
[2023-06-26 21:36:47,601] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 21:36:47,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference/checkm_data
[2023-06-26 21:36:47,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 21:36:47,632] [INFO] Task started: CheckM
[2023-06-26 21:36:47,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026398715.1_ASM2639871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026398715.1_ASM2639871v1_genomic.fna/checkm_input GCA_026398715.1_ASM2639871v1_genomic.fna/checkm_result
[2023-06-26 21:37:13,157] [INFO] Task succeeded: CheckM
[2023-06-26 21:37:13,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 12.50%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-26 21:37:13,178] [INFO] ===== Completeness check finished =====
[2023-06-26 21:37:13,178] [INFO] ===== Start GTDB Search =====
[2023-06-26 21:37:13,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026398715.1_ASM2639871v1_genomic.fna/markers.fasta)
[2023-06-26 21:37:13,179] [INFO] Task started: Blastn
[2023-06-26 21:37:13,179] [INFO] Running command: blastn -query GCA_026398715.1_ASM2639871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d979f90-7e17-44e0-bd5a-8be5957f19fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_026398715.1_ASM2639871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:37:14,593] [INFO] Task succeeded: Blastn
[2023-06-26 21:37:14,597] [INFO] Selected 21 target genomes.
[2023-06-26 21:37:14,597] [INFO] Target genome list was writen to GCA_026398715.1_ASM2639871v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 21:37:14,607] [INFO] Task started: fastANI
[2023-06-26 21:37:14,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg211c170a-65f6-4f7f-916d-fd5e19c4da1b/GCA_026398715.1_ASM2639871v1_genomic.fna.gz --refList GCA_026398715.1_ASM2639871v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026398715.1_ASM2639871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 21:37:27,560] [INFO] Task succeeded: fastANI
[2023-06-26 21:37:27,573] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 21:37:27,574] [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_001801685.1	s__Arenimonas sp001801685	88.8114	689	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420545.1	s__Arenimonas oryziterrae	80.0647	416	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000747075.1	s__Arenimonas malthae	79.9824	378	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	79.9581	365	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	79.8581	398	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643775.1	s__Arenimonas soli	79.8407	368	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241895.1	s__Arenimonas sp003241895	79.7995	380	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	79.7448	400	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	79.6114	359	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	79.5917	380	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638745.1	s__Arenimonas maotaiensis	79.1229	274	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	78.9844	308	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_900114355.1	s__Lysobacter sp900114355	78.6004	323	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	78.5277	261	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_014202935.1	s__Rehaibacterium terrae	78.4151	304	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	78.2969	304	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333835.1	s__Silanimonas sp018333835	78.2944	217	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396975.1	s__Thermomonas carbonis	78.1788	262	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014202825.1	s__Chiayiivirga flava	78.1167	273	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Chiayiivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007667275.1	s__Stenotrophomonas maltophilia_AE	78.0668	238	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.01	98.01	0.93	0.93	2	-
GCF_001700965.1	s__Stenotrophomonas nitritireducens_A	77.7398	216	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-26 21:37:27,576] [INFO] GTDB search result was written to GCA_026398715.1_ASM2639871v1_genomic.fna/result_gtdb.tsv
[2023-06-26 21:37:27,576] [INFO] ===== GTDB Search completed =====
[2023-06-26 21:37:27,583] [INFO] DFAST_QC result json was written to GCA_026398715.1_ASM2639871v1_genomic.fna/dqc_result.json
[2023-06-26 21:37:27,583] [INFO] DFAST_QC completed!
[2023-06-26 21:37:27,583] [INFO] Total running time: 0h1m1s