[2024-01-24 11:58:57,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference
[2024-01-24 11:58:58,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,418] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg534da4ca-9141-4bb8-902b-1bd8a66a1ea0/GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/cds.fna -a GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:10,766] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:10,767] [INFO] Task started: HMMsearch
[2024-01-24 11:59:10,767] [INFO] Running command: hmmsearch --tblout GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference/reference_markers.hmm GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:11,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:11,110] [INFO] Found 6/6 markers.
[2024-01-24 11:59:11,153] [INFO] Query marker FASTA was written to GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:59:11,153] [INFO] Task started: Blastn
[2024-01-24 11:59:11,153] [INFO] Running command: blastn -query GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference/reference_markers.fasta -out GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:12,074] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:12,077] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:12,078] [INFO] Target genome list was writen to GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:59:12,083] [INFO] Task started: fastANI
[2024-01-24 11:59:12,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg534da4ca-9141-4bb8-902b-1bd8a66a1ea0/GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna.gz --refList GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:24,421] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:24,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:24,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:24,432] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:24,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:24,433] [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 guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	100.0	1376	1377	95	conclusive
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	84.445	1046	1377	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	84.4427	1051	1377	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	81.5466	861	1377	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	81.3161	827	1377	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	81.1198	797	1377	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	80.9866	759	1377	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	80.6463	720	1377	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	80.4727	713	1377	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.4185	793	1377	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	80.0378	750	1377	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	79.6745	638	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:24,435] [INFO] DFAST Taxonomy check result was written to GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:59:24,436] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:24,436] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:24,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference/checkm_data
[2024-01-24 11:59:24,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:24,482] [INFO] Task started: CheckM
[2024-01-24 11:59:24,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/checkm_input GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:00:03,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:03,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:03,549] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:03,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:03,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:00:03,550] [INFO] Task started: Blastn
[2024-01-24 12:00:03,550] [INFO] Running command: blastn -query GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd49af71-5e26-4f31-b319-48951c0a8903/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:05,112] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:05,123] [INFO] Selected 11 target genomes.
[2024-01-24 12:00:05,123] [INFO] Target genome list was writen to GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:05,143] [INFO] Task started: fastANI
[2024-01-24 12:00:05,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg534da4ca-9141-4bb8-902b-1bd8a66a1ea0/GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna.gz --refList GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:16,014] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:16,024] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:16,025] [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_900113745.1	s__Pseudomonas_E guineae	100.0	1376	1377	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
GCA_018816095.1	s__Pseudomonas_E sp018816095	87.768	964	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_004920405.1	s__Pseudomonas_E leptonychotis	85.3686	1082	1377	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_002840155.1	s__Pseudomonas_E sp002840155	85.3085	1052	1377	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_018827205.1	s__Pseudomonas_E sp018827205	84.5785	945	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_900105355.1	s__Pseudomonas_E anguilliseptica	84.5402	1037	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCF_900099645.1	s__Pseudomonas_E peli	84.4398	1052	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCA_017886405.1	s__Pseudomonas_E sp017886405	84.0867	698	1377	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_002354655.1	s__Pseudomonas_E sp002354655	82.1326	897	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_013184545.1	s__Pseudomonas_E sp013184545	81.5313	863	1377	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_002025205.1	s__Pseudomonas_E sp002025205	81.4325	876	1377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:16,027] [INFO] GTDB search result was written to GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:16,028] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:16,031] [INFO] DFAST_QC result json was written to GCF_900113745.1_IMG-taxon_2667527413_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:00:16,032] [INFO] DFAST_QC completed!
[2024-01-24 12:00:16,032] [INFO] Total running time: 0h1m19s