[2024-01-24 11:30:49,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference
[2024-01-24 11:30:50,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,680] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg51aa8c77-5369-4c03-a70e-afc2ebfde8af/GCF_014268805.2_ASM1426880v2_genomic.fna.gz | prodigal -d GCF_014268805.2_ASM1426880v2_genomic.fna/cds.fna -a GCF_014268805.2_ASM1426880v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:08,024] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:08,024] [INFO] Task started: HMMsearch
[2024-01-24 11:31:08,024] [INFO] Running command: hmmsearch --tblout GCF_014268805.2_ASM1426880v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference/reference_markers.hmm GCF_014268805.2_ASM1426880v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:08,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:08,315] [INFO] Found 6/6 markers.
[2024-01-24 11:31:08,361] [INFO] Query marker FASTA was written to GCF_014268805.2_ASM1426880v2_genomic.fna/markers.fasta
[2024-01-24 11:31:08,362] [INFO] Task started: Blastn
[2024-01-24 11:31:08,362] [INFO] Running command: blastn -query GCF_014268805.2_ASM1426880v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference/reference_markers.fasta -out GCF_014268805.2_ASM1426880v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:09,380] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:09,384] [INFO] Selected 16 target genomes.
[2024-01-24 11:31:09,384] [INFO] Target genome list was writen to GCF_014268805.2_ASM1426880v2_genomic.fna/target_genomes.txt
[2024-01-24 11:31:09,396] [INFO] Task started: fastANI
[2024-01-24 11:31:09,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg51aa8c77-5369-4c03-a70e-afc2ebfde8af/GCF_014268805.2_ASM1426880v2_genomic.fna.gz --refList GCF_014268805.2_ASM1426880v2_genomic.fna/target_genomes.txt --output GCF_014268805.2_ASM1426880v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:35,365] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:35,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:35,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:35,391] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:31:35,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:35,391] [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 farsensis	strain=SWRI107	GCA_014268805.2	2745492	2745492	type	True	100.0	1742	1746	95	conclusive
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	87.6873	1386	1746	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	87.5959	1417	1746	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	86.6422	1260	1746	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	86.6181	1247	1746	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	86.6118	1300	1746	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	86.286	1271	1746	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	86.2063	1256	1746	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	86.1932	1279	1746	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	86.1518	1253	1746	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	86.1273	1141	1746	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	86.1127	1216	1746	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	85.9472	1260	1746	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	85.4058	1118	1746	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	85.1478	1256	1746	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	85.1068	1226	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:35,392] [INFO] DFAST Taxonomy check result was written to GCF_014268805.2_ASM1426880v2_genomic.fna/tc_result.tsv
[2024-01-24 11:31:35,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:35,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:35,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference/checkm_data
[2024-01-24 11:31:35,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:35,446] [INFO] Task started: CheckM
[2024-01-24 11:31:35,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268805.2_ASM1426880v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268805.2_ASM1426880v2_genomic.fna/checkm_input GCF_014268805.2_ASM1426880v2_genomic.fna/checkm_result
[2024-01-24 11:32:25,733] [INFO] Task succeeded: CheckM
[2024-01-24 11:32:25,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:32:25,757] [INFO] ===== Completeness check finished =====
[2024-01-24 11:32:25,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:32:25,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268805.2_ASM1426880v2_genomic.fna/markers.fasta)
[2024-01-24 11:32:25,758] [INFO] Task started: Blastn
[2024-01-24 11:32:25,758] [INFO] Running command: blastn -query GCF_014268805.2_ASM1426880v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d672c64-cb82-4e85-a895-05d19b685273/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268805.2_ASM1426880v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:27,580] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:27,586] [INFO] Selected 17 target genomes.
[2024-01-24 11:32:27,586] [INFO] Target genome list was writen to GCF_014268805.2_ASM1426880v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:27,625] [INFO] Task started: fastANI
[2024-01-24 11:32:27,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg51aa8c77-5369-4c03-a70e-afc2ebfde8af/GCF_014268805.2_ASM1426880v2_genomic.fna.gz --refList GCF_014268805.2_ASM1426880v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268805.2_ASM1426880v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:54,106] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:54,132] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:54,132] [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_014268825.1	s__Pseudomonas_E sp014268825	98.641	1541	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.73	98.73	0.93	0.93	2	conclusive
GCF_019139835.1	s__Pseudomonas_E sp019139835	87.5795	1417	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.50	95.50	0.87	0.87	2	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	86.653	1259	1746	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_003231305.1	s__Pseudomonas_E sichuanensis	86.5989	1250	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_015354575.1	s__Pseudomonas_E sp015354575	86.4291	1286	1746	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	86.3994	1278	1746	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	86.3582	1244	1746	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_004519305.1	s__Pseudomonas_E sp004519305	86.2427	1214	1746	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_019139675.1	s__Pseudomonas_E sp019139675	86.1714	1256	1746	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_013373935.1	s__Pseudomonas_E sp002438125	86.1269	1140	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_900110655.1	s__Pseudomonas_E soli	85.9403	1261	1746	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_011752565.1	s__Pseudomonas_E sp011752565	85.6633	1263	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.50	98.50	0.88	0.88	2	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	85.5415	1190	1746	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_000282535.1	s__Pseudomonas_E sp000282535	85.4493	1075	1746	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_016648105.1	s__Pseudomonas_E sp016648105	85.2974	1198	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428805.1	s__Pseudomonas_E sp003428805	85.1444	1242	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_013393325.1	s__Pseudomonas_E putida_P	84.9078	1223	1746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	99.27	0.91	0.82	10	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:54,134] [INFO] GTDB search result was written to GCF_014268805.2_ASM1426880v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:54,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:54,138] [INFO] DFAST_QC result json was written to GCF_014268805.2_ASM1426880v2_genomic.fna/dqc_result.json
[2024-01-24 11:32:54,138] [INFO] DFAST_QC completed!
[2024-01-24 11:32:54,138] [INFO] Total running time: 0h2m5s