[2024-01-24 11:26:11,832] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference
[2024-01-24 11:26:13,179] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,180] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg726d7706-3c1e-4ff2-a508-891e154aed80/GCF_024498955.1_ASM2449895v1_genomic.fna.gz | prodigal -d GCF_024498955.1_ASM2449895v1_genomic.fna/cds.fna -a GCF_024498955.1_ASM2449895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:23,289] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:23,289] [INFO] Task started: HMMsearch
[2024-01-24 11:26:23,289] [INFO] Running command: hmmsearch --tblout GCF_024498955.1_ASM2449895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference/reference_markers.hmm GCF_024498955.1_ASM2449895v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:23,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:23,555] [INFO] Found 6/6 markers.
[2024-01-24 11:26:23,580] [INFO] Query marker FASTA was written to GCF_024498955.1_ASM2449895v1_genomic.fna/markers.fasta
[2024-01-24 11:26:23,580] [INFO] Task started: Blastn
[2024-01-24 11:26:23,581] [INFO] Running command: blastn -query GCF_024498955.1_ASM2449895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference/reference_markers.fasta -out GCF_024498955.1_ASM2449895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:24,533] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:24,536] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:24,537] [INFO] Target genome list was writen to GCF_024498955.1_ASM2449895v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:24,542] [INFO] Task started: fastANI
[2024-01-24 11:26:24,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg726d7706-3c1e-4ff2-a508-891e154aed80/GCF_024498955.1_ASM2449895v1_genomic.fna.gz --refList GCF_024498955.1_ASM2449895v1_genomic.fna/target_genomes.txt --output GCF_024498955.1_ASM2449895v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:33,510] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:33,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:33,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:33,523] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:33,523] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:33,524] [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 fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	84.772	688	905	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	83.8781	639	905	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	83.8634	614	905	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	82.8321	619	905	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	81.8806	577	905	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	81.7818	593	905	95	below_threshold
Thermomonas beijingensis	strain=RSS-23	GCA_020034655.1	2872701	2872701	type	True	81.063	557	905	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.5286	472	905	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.3555	495	905	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.1898	452	905	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.1406	451	905	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.0726	478	905	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	79.9577	455	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:33,526] [INFO] DFAST Taxonomy check result was written to GCF_024498955.1_ASM2449895v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:33,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:33,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:33,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference/checkm_data
[2024-01-24 11:26:33,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:33,559] [INFO] Task started: CheckM
[2024-01-24 11:26:33,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498955.1_ASM2449895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498955.1_ASM2449895v1_genomic.fna/checkm_input GCF_024498955.1_ASM2449895v1_genomic.fna/checkm_result
[2024-01-24 11:27:44,685] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:44,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:44,708] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:44,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:44,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498955.1_ASM2449895v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:44,709] [INFO] Task started: Blastn
[2024-01-24 11:27:44,709] [INFO] Running command: blastn -query GCF_024498955.1_ASM2449895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ebd3d0-1e57-46ee-87cb-6ac47e31ec37/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498955.1_ASM2449895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:46,472] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:46,476] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:46,476] [INFO] Target genome list was writen to GCF_024498955.1_ASM2449895v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:46,501] [INFO] Task started: fastANI
[2024-01-24 11:27:46,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg726d7706-3c1e-4ff2-a508-891e154aed80/GCF_024498955.1_ASM2449895v1_genomic.fna.gz --refList GCF_024498955.1_ASM2449895v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498955.1_ASM2449895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:53,092] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:53,108] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:53,108] [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_014395425.1	s__Thermomonas brevis	85.0262	718	905	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	84.7676	688	905	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	84.3582	694	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	83.8443	642	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_017305095.1	s__Thermomonas sp017305095	83.5186	647	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	82.8013	623	905	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	82.6743	585	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCA_017302075.1	s__Thermomonas sp017302075	82.4348	477	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302915.1	s__Thermomonas sp011302915	82.1438	579	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396975.1	s__Thermomonas carbonis	81.7447	600	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,110] [INFO] GTDB search result was written to GCF_024498955.1_ASM2449895v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:53,111] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:53,114] [INFO] DFAST_QC result json was written to GCF_024498955.1_ASM2449895v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:53,115] [INFO] DFAST_QC completed!
[2024-01-24 11:27:53,115] [INFO] Total running time: 0h1m41s