[2024-01-24 12:14:35,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference
[2024-01-24 12:14:37,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:37,011] [INFO] Task started: Prodigal
[2024-01-24 12:14:37,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg861cce5d-ab68-4c74-9388-8053fc1ae3e5/GCF_019139535.1_ASM1913953v1_genomic.fna.gz | prodigal -d GCF_019139535.1_ASM1913953v1_genomic.fna/cds.fna -a GCF_019139535.1_ASM1913953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:00,666] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:00,666] [INFO] Task started: HMMsearch
[2024-01-24 12:15:00,666] [INFO] Running command: hmmsearch --tblout GCF_019139535.1_ASM1913953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference/reference_markers.hmm GCF_019139535.1_ASM1913953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:00,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:00,972] [INFO] Found 6/6 markers.
[2024-01-24 12:15:01,019] [INFO] Query marker FASTA was written to GCF_019139535.1_ASM1913953v1_genomic.fna/markers.fasta
[2024-01-24 12:15:01,020] [INFO] Task started: Blastn
[2024-01-24 12:15:01,020] [INFO] Running command: blastn -query GCF_019139535.1_ASM1913953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference/reference_markers.fasta -out GCF_019139535.1_ASM1913953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:02,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:02,189] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:02,189] [INFO] Target genome list was writen to GCF_019139535.1_ASM1913953v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:02,195] [INFO] Task started: fastANI
[2024-01-24 12:15:02,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg861cce5d-ab68-4c74-9388-8053fc1ae3e5/GCF_019139535.1_ASM1913953v1_genomic.fna.gz --refList GCF_019139535.1_ASM1913953v1_genomic.fna/target_genomes.txt --output GCF_019139535.1_ASM1913953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:27,276] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:27,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:27,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:27,289] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:27,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:27,290] [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
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	100.0	1841	1842	95	conclusive
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	91.6892	1597	1842	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	90.1615	1489	1842	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	90.0607	1503	1842	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	89.854	1497	1842	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	89.6005	1486	1842	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	89.3091	1481	1842	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	89.0439	1387	1842	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	88.5863	1429	1842	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	88.5428	1465	1842	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.8531	1308	1842	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.7704	1297	1842	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.448	849	1842	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.4399	681	1842	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	81.3069	839	1842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:27,292] [INFO] DFAST Taxonomy check result was written to GCF_019139535.1_ASM1913953v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:27,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:27,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:27,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference/checkm_data
[2024-01-24 12:15:27,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:27,348] [INFO] Task started: CheckM
[2024-01-24 12:15:27,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019139535.1_ASM1913953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019139535.1_ASM1913953v1_genomic.fna/checkm_input GCF_019139535.1_ASM1913953v1_genomic.fna/checkm_result
[2024-01-24 12:16:41,034] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:41,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:41,052] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:41,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:41,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019139535.1_ASM1913953v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:41,053] [INFO] Task started: Blastn
[2024-01-24 12:16:41,053] [INFO] Running command: blastn -query GCF_019139535.1_ASM1913953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdf7492e-d64a-4a6f-9de4-01c72e6cc185/dqc_reference/reference_markers_gtdb.fasta -out GCF_019139535.1_ASM1913953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:43,034] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:43,038] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:43,038] [INFO] Target genome list was writen to GCF_019139535.1_ASM1913953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:43,044] [INFO] Task started: fastANI
[2024-01-24 12:16:43,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg861cce5d-ab68-4c74-9388-8053fc1ae3e5/GCF_019139535.1_ASM1913953v1_genomic.fna.gz --refList GCF_019139535.1_ASM1913953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019139535.1_ASM1913953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:03,726] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:03,736] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:03,736] [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_019139535.1	s__Pseudomonas_E sp019139535	100.0	1841	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004519305.1	s__Pseudomonas_E sp004519305	94.2628	1581	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014268885.2	s__Pseudomonas_E sp014268885	91.7096	1595	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861355.1	s__Pseudomonas_E sp001259595	90.3734	1544	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_003205295.1	s__Pseudomonas_E mosselii_B	90.3603	1516	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_000621225.1	s__Pseudomonas_E mosselii	90.047	1504	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_019139675.1	s__Pseudomonas_E sp019139675	89.8809	1495	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110655.1	s__Pseudomonas_E soli	89.5798	1488	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCF_011752525.1	s__Pseudomonas_E sp011752525	89.3727	1426	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354575.1	s__Pseudomonas_E sp015354575	89.0534	1436	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019139835.1	s__Pseudomonas_E sp019139835	88.5361	1435	1842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.50	95.50	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:03,738] [INFO] GTDB search result was written to GCF_019139535.1_ASM1913953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:03,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:03,742] [INFO] DFAST_QC result json was written to GCF_019139535.1_ASM1913953v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:03,742] [INFO] DFAST_QC completed!
[2024-01-24 12:17:03,742] [INFO] Total running time: 0h2m28s