[2024-01-24 15:17:49,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,535] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stge6e9627c-f0d7-4a42-b298-0b2036192ebd/GCF_014268885.2_ASM1426888v2_genomic.fna.gz | prodigal -d GCF_014268885.2_ASM1426888v2_genomic.fna/cds.fna -a GCF_014268885.2_ASM1426888v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:19,002] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:19,002] [INFO] Task started: HMMsearch
[2024-01-24 15:18:19,002] [INFO] Running command: hmmsearch --tblout GCF_014268885.2_ASM1426888v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference/reference_markers.hmm GCF_014268885.2_ASM1426888v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:19,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:19,342] [INFO] Found 6/6 markers.
[2024-01-24 15:18:19,404] [INFO] Query marker FASTA was written to GCF_014268885.2_ASM1426888v2_genomic.fna/markers.fasta
[2024-01-24 15:18:19,405] [INFO] Task started: Blastn
[2024-01-24 15:18:19,405] [INFO] Running command: blastn -query GCF_014268885.2_ASM1426888v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference/reference_markers.fasta -out GCF_014268885.2_ASM1426888v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:20,423] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:20,427] [INFO] Selected 20 target genomes.
[2024-01-24 15:18:20,428] [INFO] Target genome list was writen to GCF_014268885.2_ASM1426888v2_genomic.fna/target_genomes.txt
[2024-01-24 15:18:20,440] [INFO] Task started: fastANI
[2024-01-24 15:18:20,441] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e9627c-f0d7-4a42-b298-0b2036192ebd/GCF_014268885.2_ASM1426888v2_genomic.fna.gz --refList GCF_014268885.2_ASM1426888v2_genomic.fna/target_genomes.txt --output GCF_014268885.2_ASM1426888v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:49,153] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:49,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:49,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:49,175] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:49,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:49,175] [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 xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	100.0	1866	1869	95	conclusive
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	91.7677	1602	1869	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	90.1705	1528	1869	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	90.0915	1522	1869	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	89.5114	1524	1869	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	89.2115	1485	1869	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	89.0821	1506	1869	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	88.6526	1395	1869	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	88.1777	1412	1869	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	88.1124	1411	1869	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.5036	1327	1869	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.4332	1289	1869	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.3114	799	1869	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.8048	836	1869	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.3263	656	1869	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	75.4281	93	1869	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	75.4007	83	1869	95	below_threshold
Microterricola pindariensis	strain=PON 10	GCA_002936985.1	478010	478010	type	True	75.1725	70	1869	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:49,177] [INFO] DFAST Taxonomy check result was written to GCF_014268885.2_ASM1426888v2_genomic.fna/tc_result.tsv
[2024-01-24 15:18:49,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:49,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:49,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference/checkm_data
[2024-01-24 15:18:49,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:49,235] [INFO] Task started: CheckM
[2024-01-24 15:18:49,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268885.2_ASM1426888v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268885.2_ASM1426888v2_genomic.fna/checkm_input GCF_014268885.2_ASM1426888v2_genomic.fna/checkm_result
[2024-01-24 15:20:07,228] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:07,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:07,254] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:07,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:07,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268885.2_ASM1426888v2_genomic.fna/markers.fasta)
[2024-01-24 15:20:07,255] [INFO] Task started: Blastn
[2024-01-24 15:20:07,255] [INFO] Running command: blastn -query GCF_014268885.2_ASM1426888v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg947e3762-b6ff-4699-84c0-60edc80b00d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268885.2_ASM1426888v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:08,983] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:08,987] [INFO] Selected 14 target genomes.
[2024-01-24 15:20:08,987] [INFO] Target genome list was writen to GCF_014268885.2_ASM1426888v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:08,998] [INFO] Task started: fastANI
[2024-01-24 15:20:08,999] [INFO] Running command: fastANI --query /var/lib/cwl/stge6e9627c-f0d7-4a42-b298-0b2036192ebd/GCF_014268885.2_ASM1426888v2_genomic.fna.gz --refList GCF_014268885.2_ASM1426888v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268885.2_ASM1426888v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:32,133] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:32,152] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:32,153] [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_014268885.2	s__Pseudomonas_E sp014268885	100.0	1865	1869	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_019139535.1	s__Pseudomonas_E sp019139535	91.7602	1602	1869	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_004519305.1	s__Pseudomonas_E sp004519305	91.5295	1545	1869	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_003205295.1	s__Pseudomonas_E mosselii_B	90.3533	1512	1869	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_016861355.1	s__Pseudomonas_E sp001259595	90.3063	1548	1869	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_000621225.1	s__Pseudomonas_E mosselii	90.0827	1523	1869	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	89.5081	1523	1869	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_018417595.1	s__Pseudomonas_E entomophila_C	89.1273	1515	1869	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_011752525.1	s__Pseudomonas_E sp011752525	88.9477	1424	1869	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	88.7491	1443	1869	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_900105185.1	s__Pseudomonas_E saponiphila	82.3527	1144	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
GCF_013385635.1	s__Pseudomonas_E gingeri_A	82.0535	1079	1869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.63	99.24	0.97	0.93	14	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:32,154] [INFO] GTDB search result was written to GCF_014268885.2_ASM1426888v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:32,155] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:32,160] [INFO] DFAST_QC result json was written to GCF_014268885.2_ASM1426888v2_genomic.fna/dqc_result.json
[2024-01-24 15:20:32,160] [INFO] DFAST_QC completed!
[2024-01-24 15:20:32,160] [INFO] Total running time: 0h2m43s