[2024-01-25 18:39:50,730] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference
[2024-01-25 18:39:51,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,925] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dc1d0a4-0900-4c0f-9637-0176f21d6c46/GCF_028201335.1_ASM2820133v1_genomic.fna.gz | prodigal -d GCF_028201335.1_ASM2820133v1_genomic.fna/cds.fna -a GCF_028201335.1_ASM2820133v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:59,914] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:59,914] [INFO] Task started: HMMsearch
[2024-01-25 18:39:59,915] [INFO] Running command: hmmsearch --tblout GCF_028201335.1_ASM2820133v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference/reference_markers.hmm GCF_028201335.1_ASM2820133v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:00,128] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:00,129] [INFO] Found 6/6 markers.
[2024-01-25 18:40:00,155] [INFO] Query marker FASTA was written to GCF_028201335.1_ASM2820133v1_genomic.fna/markers.fasta
[2024-01-25 18:40:00,156] [INFO] Task started: Blastn
[2024-01-25 18:40:00,156] [INFO] Running command: blastn -query GCF_028201335.1_ASM2820133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference/reference_markers.fasta -out GCF_028201335.1_ASM2820133v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:00,996] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:00,999] [INFO] Selected 24 target genomes.
[2024-01-25 18:40:00,999] [INFO] Target genome list was writen to GCF_028201335.1_ASM2820133v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:01,010] [INFO] Task started: fastANI
[2024-01-25 18:40:01,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dc1d0a4-0900-4c0f-9637-0176f21d6c46/GCF_028201335.1_ASM2820133v1_genomic.fna.gz --refList GCF_028201335.1_ASM2820133v1_genomic.fna/target_genomes.txt --output GCF_028201335.1_ASM2820133v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:18,567] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:18,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:18,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:18,581] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:40:18,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:40:18,582] [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 aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	85.6202	738	952	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	84.2243	593	952	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	84.2035	607	952	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	84.0061	659	952	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	83.7208	709	952	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	83.5653	714	952	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	82.4237	555	952	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	82.1167	536	952	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	82.0938	577	952	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.8286	542	952	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.7878	590	952	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	81.7232	569	952	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.6655	572	952	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	81.6588	569	952	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.6507	591	952	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	81.5491	555	952	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.5205	592	952	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	81.132	568	952	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	81.0409	514	952	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	80.8169	518	952	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	80.7439	557	952	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.7795	175	952	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.7603	218	952	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	75.7355	71	952	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:18,583] [INFO] DFAST Taxonomy check result was written to GCF_028201335.1_ASM2820133v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:18,584] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:18,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:18,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference/checkm_data
[2024-01-25 18:40:18,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:18,620] [INFO] Task started: CheckM
[2024-01-25 18:40:18,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028201335.1_ASM2820133v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028201335.1_ASM2820133v1_genomic.fna/checkm_input GCF_028201335.1_ASM2820133v1_genomic.fna/checkm_result
[2024-01-25 18:41:07,992] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:07,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:08,045] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:08,045] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:08,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028201335.1_ASM2820133v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:08,046] [INFO] Task started: Blastn
[2024-01-25 18:41:08,046] [INFO] Running command: blastn -query GCF_028201335.1_ASM2820133v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f66e0e0-eeca-434b-bdf5-b6f0c16e8f81/dqc_reference/reference_markers_gtdb.fasta -out GCF_028201335.1_ASM2820133v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:09,639] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:09,641] [INFO] Selected 19 target genomes.
[2024-01-25 18:41:09,642] [INFO] Target genome list was writen to GCF_028201335.1_ASM2820133v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:09,671] [INFO] Task started: fastANI
[2024-01-25 18:41:09,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dc1d0a4-0900-4c0f-9637-0176f21d6c46/GCF_028201335.1_ASM2820133v1_genomic.fna.gz --refList GCF_028201335.1_ASM2820133v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028201335.1_ASM2820133v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:23,094] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:23,105] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:23,106] [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_017302075.1	s__Thermomonas sp017302075	97.15	698	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017302095.1	s__Thermomonas sp017302095	90.8308	517	952	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	85.6109	739	952	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	85.199	711	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_014395425.1	s__Thermomonas brevis	84.6745	659	952	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	84.1821	609	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000423885.1	s__Thermomonas fusca	83.9921	660	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCA_017305095.1	s__Thermomonas sp017305095	83.882	617	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014678725.1	s__Thermomonas sp014678725	83.7965	664	952	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	83.587	712	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011302915.1	s__Thermomonas sp011302915	83.5466	672	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513955.1	s__Pseudoxanthomonas suwonensis_C	81.7581	592	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	98.37	96.94	0.95	0.91	3	-
GCF_001431595.1	s__Stenotrophomonas acidaminiphila	81.418	522	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	-
GCA_002798175.1	s__Luteimonas sp002798175	80.9673	524	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118975.1	s__Luteimonas sp004118975	80.9339	516	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145325.1	s__Lysobacter spongiae	80.9116	549	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	80.4889	514	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_001431665.1	s__Stenotrophomonas maltophilia_K	80.1619	489	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015840715.1	s__Cyanobium sp015840715	74.8901	55	952	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:23,107] [INFO] GTDB search result was written to GCF_028201335.1_ASM2820133v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:23,108] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:23,112] [INFO] DFAST_QC result json was written to GCF_028201335.1_ASM2820133v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:23,113] [INFO] DFAST_QC completed!
[2024-01-25 18:41:23,113] [INFO] Total running time: 0h1m32s