[2024-01-25 20:18:21,183] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:21,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:21,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference
[2024-01-25 20:18:22,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:22,362] [INFO] Task started: Prodigal
[2024-01-25 20:18:22,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a710902-10f9-4d22-9ad9-6516552b921f/GCF_026072635.1_ASM2607263v1_genomic.fna.gz | prodigal -d GCF_026072635.1_ASM2607263v1_genomic.fna/cds.fna -a GCF_026072635.1_ASM2607263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:46,505] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:46,505] [INFO] Task started: HMMsearch
[2024-01-25 20:18:46,505] [INFO] Running command: hmmsearch --tblout GCF_026072635.1_ASM2607263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference/reference_markers.hmm GCF_026072635.1_ASM2607263v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:46,801] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:46,802] [INFO] Found 6/6 markers.
[2024-01-25 20:18:46,854] [INFO] Query marker FASTA was written to GCF_026072635.1_ASM2607263v1_genomic.fna/markers.fasta
[2024-01-25 20:18:46,854] [INFO] Task started: Blastn
[2024-01-25 20:18:46,854] [INFO] Running command: blastn -query GCF_026072635.1_ASM2607263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference/reference_markers.fasta -out GCF_026072635.1_ASM2607263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:47,831] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:47,834] [INFO] Selected 22 target genomes.
[2024-01-25 20:18:47,834] [INFO] Target genome list was writen to GCF_026072635.1_ASM2607263v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:47,841] [INFO] Task started: fastANI
[2024-01-25 20:18:47,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a710902-10f9-4d22-9ad9-6516552b921f/GCF_026072635.1_ASM2607263v1_genomic.fna.gz --refList GCF_026072635.1_ASM2607263v1_genomic.fna/target_genomes.txt --output GCF_026072635.1_ASM2607263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:17,709] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:17,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:17,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:17,723] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:19:17,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:19:17,723] [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 tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	92.8858	1960	2220	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	87.5826	1625	2220	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	84.9891	1276	2220	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	84.9786	1257	2220	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	83.8575	1038	2220	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	83.8473	1076	2220	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.6899	1009	2220	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	83.2523	920	2220	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	83.2252	1107	2220	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	83.2122	1082	2220	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	83.1927	1115	2220	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	83.1535	1119	2220	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	82.5402	1220	2220	95	below_threshold
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	82.5163	1252	2220	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	82.4748	1235	2220	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	82.4735	1234	2220	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	81.7094	760	2220	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.2577	809	2220	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	80.3787	943	2220	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	80.3494	911	2220	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	80.2742	985	2220	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	79.7514	824	2220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:17,727] [INFO] DFAST Taxonomy check result was written to GCF_026072635.1_ASM2607263v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:17,728] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:17,728] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:17,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference/checkm_data
[2024-01-25 20:19:17,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:17,790] [INFO] Task started: CheckM
[2024-01-25 20:19:17,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026072635.1_ASM2607263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026072635.1_ASM2607263v1_genomic.fna/checkm_input GCF_026072635.1_ASM2607263v1_genomic.fna/checkm_result
[2024-01-25 20:20:32,234] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:32,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:32,257] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:32,257] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:32,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026072635.1_ASM2607263v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:32,259] [INFO] Task started: Blastn
[2024-01-25 20:20:32,259] [INFO] Running command: blastn -query GCF_026072635.1_ASM2607263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg759099b6-d23f-44d5-8e74-131fef12c4c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_026072635.1_ASM2607263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:34,154] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:34,157] [INFO] Selected 18 target genomes.
[2024-01-25 20:20:34,157] [INFO] Target genome list was writen to GCF_026072635.1_ASM2607263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:34,260] [INFO] Task started: fastANI
[2024-01-25 20:20:34,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a710902-10f9-4d22-9ad9-6516552b921f/GCF_026072635.1_ASM2607263v1_genomic.fna.gz --refList GCF_026072635.1_ASM2607263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026072635.1_ASM2607263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:02,391] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:02,402] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:02,402] [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_000474255.1	s__Pseudomonas_F alcaligenes_A	98.6948	2018	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	conclusive
GCF_012767755.2	s__Pseudomonas_F sp003234055	92.893	1960	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_900111835.1	s__Pseudomonas_F otitidis	87.5849	1625	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.35	95.43	0.89	0.84	21	-
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	85.5541	1381	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	85.0328	1312	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014700075.1	s__Pseudomonas_F sp014700075	85.0187	1297	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001708505.1	s__Pseudomonas_F sp001708505	84.458	1252	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	84.3641	1301	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	84.3364	1018	2220	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_005508865.1	s__Pseudomonas_E sp005508865	84.1098	1111	2220	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_902506505.1	s__Pseudomonas_E sp902506505	84.1025	1022	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	84.061	1114	2220	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_002483005.1	s__Pseudomonas_E sp002483005	84.0477	614	2220	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_900103845.1	s__Pseudomonas jinjuensis	83.1999	1111	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017589465.1	s__Pseudomonas sp017589465	83.0114	1053	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113905.1	s__Pseudomonas_E argentinensis	81.7602	964	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003253735.1	s__Pseudomonas_E sp003253735	81.7029	973	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.95	0.95	2	-
GCF_013408425.1	s__Pseudomonas_E fulva_A	81.3664	976	2220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	99.00	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:02,405] [INFO] GTDB search result was written to GCF_026072635.1_ASM2607263v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:02,405] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:02,408] [INFO] DFAST_QC result json was written to GCF_026072635.1_ASM2607263v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:02,409] [INFO] DFAST_QC completed!
[2024-01-25 20:21:02,409] [INFO] Total running time: 0h2m41s