[2024-01-24 11:48:21,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:48:21,281] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:48:21,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference
[2024-01-24 11:48:24,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:48:24,566] [INFO] Task started: Prodigal
[2024-01-24 11:48:24,567] [INFO] Running command: gunzip -c /var/lib/cwl/stg142870f9-8ae2-4507-af8c-09d238fa04e5/GCF_014396975.1_ASM1439697v1_genomic.fna.gz | prodigal -d GCF_014396975.1_ASM1439697v1_genomic.fna/cds.fna -a GCF_014396975.1_ASM1439697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:48:36,765] [INFO] Task succeeded: Prodigal
[2024-01-24 11:48:36,766] [INFO] Task started: HMMsearch
[2024-01-24 11:48:36,766] [INFO] Running command: hmmsearch --tblout GCF_014396975.1_ASM1439697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference/reference_markers.hmm GCF_014396975.1_ASM1439697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:48:37,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:48:37,031] [INFO] Found 6/6 markers.
[2024-01-24 11:48:37,062] [INFO] Query marker FASTA was written to GCF_014396975.1_ASM1439697v1_genomic.fna/markers.fasta
[2024-01-24 11:48:37,062] [INFO] Task started: Blastn
[2024-01-24 11:48:37,062] [INFO] Running command: blastn -query GCF_014396975.1_ASM1439697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference/reference_markers.fasta -out GCF_014396975.1_ASM1439697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:48:38,021] [INFO] Task succeeded: Blastn
[2024-01-24 11:48:38,025] [INFO] Selected 14 target genomes.
[2024-01-24 11:48:38,026] [INFO] Target genome list was writen to GCF_014396975.1_ASM1439697v1_genomic.fna/target_genomes.txt
[2024-01-24 11:48:38,032] [INFO] Task started: fastANI
[2024-01-24 11:48:38,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg142870f9-8ae2-4507-af8c-09d238fa04e5/GCF_014396975.1_ASM1439697v1_genomic.fna.gz --refList GCF_014396975.1_ASM1439697v1_genomic.fna/target_genomes.txt --output GCF_014396975.1_ASM1439697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:48:49,656] [INFO] Task succeeded: fastANI
[2024-01-24 11:48:49,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:48:49,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:48:49,674] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:48:49,675] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:48:49,675] [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
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	100.0	1151	1152	95	conclusive
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	99.9705	1139	1152	95	conclusive
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	85.0135	752	1152	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	82.7858	673	1152	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	82.4274	575	1152	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	82.3445	606	1152	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.7147	585	1152	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.6033	627	1152	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.5057	514	1152	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.4952	586	1152	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.3098	599	1152	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.1729	570	1152	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	80.0856	561	1152	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	80.031	537	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:48:49,681] [INFO] DFAST Taxonomy check result was written to GCF_014396975.1_ASM1439697v1_genomic.fna/tc_result.tsv
[2024-01-24 11:48:49,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:48:49,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:48:49,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference/checkm_data
[2024-01-24 11:48:49,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:48:49,724] [INFO] Task started: CheckM
[2024-01-24 11:48:49,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014396975.1_ASM1439697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014396975.1_ASM1439697v1_genomic.fna/checkm_input GCF_014396975.1_ASM1439697v1_genomic.fna/checkm_result
[2024-01-24 11:49:50,499] [INFO] Task succeeded: CheckM
[2024-01-24 11:49:50,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:49:50,519] [INFO] ===== Completeness check finished =====
[2024-01-24 11:49:50,519] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:49:50,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014396975.1_ASM1439697v1_genomic.fna/markers.fasta)
[2024-01-24 11:49:50,520] [INFO] Task started: Blastn
[2024-01-24 11:49:50,521] [INFO] Running command: blastn -query GCF_014396975.1_ASM1439697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3da0b164-d98d-4a09-a2fa-1bdc67fe259c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014396975.1_ASM1439697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:49:52,267] [INFO] Task succeeded: Blastn
[2024-01-24 11:49:52,271] [INFO] Selected 13 target genomes.
[2024-01-24 11:49:52,271] [INFO] Target genome list was writen to GCF_014396975.1_ASM1439697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:49:52,282] [INFO] Task started: fastANI
[2024-01-24 11:49:52,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg142870f9-8ae2-4507-af8c-09d238fa04e5/GCF_014396975.1_ASM1439697v1_genomic.fna.gz --refList GCF_014396975.1_ASM1439697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014396975.1_ASM1439697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:50:03,010] [INFO] Task succeeded: fastANI
[2024-01-24 11:50:03,025] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:50:03,026] [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
GCF_014396975.1	s__Thermomonas carbonis	100.0	1151	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_006337105.1	s__Thermomonas sp006337105	85.011	755	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	84.6218	693	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_011302915.1	s__Thermomonas sp011302915	83.8502	705	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	83.6966	590	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	83.4547	457	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	83.2244	728	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	82.8326	670	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_014678725.1	s__Thermomonas sp014678725	82.7889	680	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003505795.1	s__UBA8801 sp003505795	80.9138	367	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__UBA8801	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830035.1	s__Luteimonas_C cucumeris	80.5053	585	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851915.1	s__Pseudoxanthomonas sp014851915	80.4484	579	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104255.1	s__Pseudoxanthomonas_A sp900104255	80.4059	586	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:50:03,027] [INFO] GTDB search result was written to GCF_014396975.1_ASM1439697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:50:03,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:50:03,031] [INFO] DFAST_QC result json was written to GCF_014396975.1_ASM1439697v1_genomic.fna/dqc_result.json
[2024-01-24 11:50:03,031] [INFO] DFAST_QC completed!
[2024-01-24 11:50:03,031] [INFO] Total running time: 0h1m42s