[2024-01-24 15:10:36,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:36,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:36,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference
[2024-01-24 15:10:40,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,102] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,103] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4050bb3-0bf7-4841-a9d2-81cea9328531/GCF_903652925.1_LMG_26857_genomic.fna.gz | prodigal -d GCF_903652925.1_LMG_26857_genomic.fna/cds.fna -a GCF_903652925.1_LMG_26857_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:07,990] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:07,990] [INFO] Task started: HMMsearch
[2024-01-24 15:11:07,990] [INFO] Running command: hmmsearch --tblout GCF_903652925.1_LMG_26857_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference/reference_markers.hmm GCF_903652925.1_LMG_26857_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:08,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:08,418] [INFO] Found 6/6 markers.
[2024-01-24 15:11:08,479] [INFO] Query marker FASTA was written to GCF_903652925.1_LMG_26857_genomic.fna/markers.fasta
[2024-01-24 15:11:08,479] [INFO] Task started: Blastn
[2024-01-24 15:11:08,479] [INFO] Running command: blastn -query GCF_903652925.1_LMG_26857_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference/reference_markers.fasta -out GCF_903652925.1_LMG_26857_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:09,647] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:09,650] [INFO] Selected 21 target genomes.
[2024-01-24 15:11:09,650] [INFO] Target genome list was writen to GCF_903652925.1_LMG_26857_genomic.fna/target_genomes.txt
[2024-01-24 15:11:09,657] [INFO] Task started: fastANI
[2024-01-24 15:11:09,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4050bb3-0bf7-4841-a9d2-81cea9328531/GCF_903652925.1_LMG_26857_genomic.fna.gz --refList GCF_903652925.1_LMG_26857_genomic.fna/target_genomes.txt --output GCF_903652925.1_LMG_26857_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:39,045] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:39,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:39,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:39,064] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:39,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:39,065] [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
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	100.0	2389	2390	95	conclusive
Achromobacter aegrifaciens	strain=LMG 26852	GCA_902859735.1	1287736	1287736	type	True	91.0489	1844	2390	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	89.3056	1801	2390	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	89.3011	1808	2390	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	89.2679	1799	2390	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	89.2576	1799	2390	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	88.5277	1543	2390	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	86.5022	1534	2390	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.8473	917	2390	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.8993	472	2390	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.8984	478	2390	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.6455	368	2390	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	77.4308	595	2390	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	77.4059	564	2390	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	77.3747	367	2390	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	77.3547	446	2390	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.2643	454	2390	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	77.1311	477	2390	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	77.1217	444	2390	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.1164	467	2390	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.1118	592	2390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:39,067] [INFO] DFAST Taxonomy check result was written to GCF_903652925.1_LMG_26857_genomic.fna/tc_result.tsv
[2024-01-24 15:11:39,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:39,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:39,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference/checkm_data
[2024-01-24 15:11:39,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:39,144] [INFO] Task started: CheckM
[2024-01-24 15:11:39,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903652925.1_LMG_26857_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903652925.1_LMG_26857_genomic.fna/checkm_input GCF_903652925.1_LMG_26857_genomic.fna/checkm_result
[2024-01-24 15:12:52,568] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:52,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:52,595] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:52,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:52,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903652925.1_LMG_26857_genomic.fna/markers.fasta)
[2024-01-24 15:12:52,596] [INFO] Task started: Blastn
[2024-01-24 15:12:52,596] [INFO] Running command: blastn -query GCF_903652925.1_LMG_26857_genomic.fna/markers.fasta -db /var/lib/cwl/stg33b78aa7-d4b2-4163-9e2b-f6cdb714ecf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_903652925.1_LMG_26857_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:54,705] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:54,710] [INFO] Selected 17 target genomes.
[2024-01-24 15:12:54,710] [INFO] Target genome list was writen to GCF_903652925.1_LMG_26857_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:54,723] [INFO] Task started: fastANI
[2024-01-24 15:12:54,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4050bb3-0bf7-4841-a9d2-81cea9328531/GCF_903652925.1_LMG_26857_genomic.fna.gz --refList GCF_903652925.1_LMG_26857_genomic.fna/target_genomes_gtdb.txt --output GCF_903652925.1_LMG_26857_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:20,444] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:20,460] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:20,460] [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_903652925.1	s__Achromobacter anxifer	100.0	2389	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	conclusive
GCF_014490035.1	s__Achromobacter bronchisepticus_A	91.1481	1866	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_002192695.1	s__Achromobacter xylosoxidans_C	91.1202	1880	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_902859735.1	s__Achromobacter aegrifaciens	91.0489	1844	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_013267355.1	s__Achromobacter pestifer_A	91.0484	1874	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	90.8871	1873	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_002209555.1	s__Achromobacter insolitus	89.2546	1799	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.13	98.86	0.96	0.89	17	-
GCF_900496975.1	s__Achromobacter veterisilvae	88.5368	1542	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859645.1	s__Achromobacter insuavis	87.0734	1446	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_016428875.1	s__Xylophilus sp016428875	77.5889	479	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053685.1	s__Variovorax sp003053685	77.4751	692	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	100.00	100.00	1.00	1.00	5	-
GCF_000377645.1	s__Thiomonas sp000377645	77.0702	385	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	96.94	96.87	0.91	0.90	3	-
GCF_001191005.1	s__Pseudoduganella sp001191005	77.048	454	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007994965.1	s__Piscinibacter aquaticus	77.042	412	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013369485.1	s__Pseudoduganella sp013369485	77.0279	428	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900088825.1	s__Thiomonas delicata	76.8843	270	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	98.68	98.60	0.90	0.88	3	-
GCF_000800095.1	s__Rhizobacter sp000800095	76.8783	529	2390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:20,462] [INFO] GTDB search result was written to GCF_903652925.1_LMG_26857_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:20,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:20,467] [INFO] DFAST_QC result json was written to GCF_903652925.1_LMG_26857_genomic.fna/dqc_result.json
[2024-01-24 15:13:20,467] [INFO] DFAST_QC completed!
[2024-01-24 15:13:20,468] [INFO] Total running time: 0h2m44s