[2024-01-24 15:02:24,121] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,127] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference
[2024-01-24 15:02:26,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,426] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e87a581-6f8a-40ca-876c-cdfc5e543717/GCF_030160515.1_ASM3016051v1_genomic.fna.gz | prodigal -d GCF_030160515.1_ASM3016051v1_genomic.fna/cds.fna -a GCF_030160515.1_ASM3016051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:44,824] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:44,824] [INFO] Task started: HMMsearch
[2024-01-24 15:02:44,825] [INFO] Running command: hmmsearch --tblout GCF_030160515.1_ASM3016051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference/reference_markers.hmm GCF_030160515.1_ASM3016051v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:45,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:45,155] [INFO] Found 6/6 markers.
[2024-01-24 15:02:45,202] [INFO] Query marker FASTA was written to GCF_030160515.1_ASM3016051v1_genomic.fna/markers.fasta
[2024-01-24 15:02:45,203] [INFO] Task started: Blastn
[2024-01-24 15:02:45,203] [INFO] Running command: blastn -query GCF_030160515.1_ASM3016051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference/reference_markers.fasta -out GCF_030160515.1_ASM3016051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:46,336] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:46,340] [INFO] Selected 12 target genomes.
[2024-01-24 15:02:46,340] [INFO] Target genome list was writen to GCF_030160515.1_ASM3016051v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:46,348] [INFO] Task started: fastANI
[2024-01-24 15:02:46,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e87a581-6f8a-40ca-876c-cdfc5e543717/GCF_030160515.1_ASM3016051v1_genomic.fna.gz --refList GCF_030160515.1_ASM3016051v1_genomic.fna/target_genomes.txt --output GCF_030160515.1_ASM3016051v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:03,922] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:03,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:03,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:03,935] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:03,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:03,936] [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 plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	99.9926	1736	1755	95	conclusive
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	99.9828	1705	1755	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	90.6998	1434	1755	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	90.6437	1366	1755	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	87.6861	1307	1755	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	87.599	1343	1755	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	87.4148	1350	1755	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.4112	1227	1755	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	87.3652	1306	1755	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	87.2236	1275	1755	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	87.0358	1345	1755	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	86.9406	1256	1755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:03,939] [INFO] DFAST Taxonomy check result was written to GCF_030160515.1_ASM3016051v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:03,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:03,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:03,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference/checkm_data
[2024-01-24 15:03:03,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:04,009] [INFO] Task started: CheckM
[2024-01-24 15:03:04,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160515.1_ASM3016051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160515.1_ASM3016051v1_genomic.fna/checkm_input GCF_030160515.1_ASM3016051v1_genomic.fna/checkm_result
[2024-01-24 15:04:01,809] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:01,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:01,838] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:01,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:01,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160515.1_ASM3016051v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:01,840] [INFO] Task started: Blastn
[2024-01-24 15:04:01,840] [INFO] Running command: blastn -query GCF_030160515.1_ASM3016051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb514f3d-983d-4f27-957c-b7f9b79309f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160515.1_ASM3016051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:04,114] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:04,117] [INFO] Selected 15 target genomes.
[2024-01-24 15:04:04,117] [INFO] Target genome list was writen to GCF_030160515.1_ASM3016051v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:04,129] [INFO] Task started: fastANI
[2024-01-24 15:04:04,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e87a581-6f8a-40ca-876c-cdfc5e543717/GCF_030160515.1_ASM3016051v1_genomic.fna.gz --refList GCF_030160515.1_ASM3016051v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160515.1_ASM3016051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:26,826] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:26,838] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:26,839] [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_000730665.1	s__Pseudomonas_E plecoglossicida	99.9828	1705	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	conclusive
GCF_000282535.1	s__Pseudomonas_E sp000282535	91.532	1342	1755	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	90.6556	1365	1755	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_002112505.1	s__Pseudomonas_E sp002112505	88.7046	1406	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_002025705.1	s__Pseudomonas_E putida_J	88.3006	1397	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.29	96.26	0.90	0.90	5	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	88.0652	1316	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	87.8118	1335	1755	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_001320525.1	s__Pseudomonas_E sp001320525	87.6723	1295	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	98.78	0.89	0.86	10	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	87.4551	1268	1755	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_000019445.1	s__Pseudomonas_E putida_E	87.4192	1312	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_000731675.1	s__Pseudomonas_E capeferrum	87.4149	1350	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_014269185.2	s__Pseudomonas_E sp014269185	87.2266	1275	1755	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_002736125.1	s__Pseudomonas_E putida_M	87.1089	1363	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
GCF_014268885.2	s__Pseudomonas_E sp014268885	86.9437	1256	1755	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_004357765.1	s__Pseudomonas_E putida_U	86.2816	1243	1755	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:26,841] [INFO] GTDB search result was written to GCF_030160515.1_ASM3016051v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:26,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:26,845] [INFO] DFAST_QC result json was written to GCF_030160515.1_ASM3016051v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:26,845] [INFO] DFAST_QC completed!
[2024-01-24 15:04:26,845] [INFO] Total running time: 0h2m3s