[2024-01-24 12:06:33,285] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference
[2024-01-24 12:06:34,545] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:34,545] [INFO] Task started: Prodigal
[2024-01-24 12:06:34,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg841e3e21-c9d3-47c3-b157-0e14cb1f9ac7/GCF_014269035.2_ASM1426903v2_genomic.fna.gz | prodigal -d GCF_014269035.2_ASM1426903v2_genomic.fna/cds.fna -a GCF_014269035.2_ASM1426903v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:53,804] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:53,805] [INFO] Task started: HMMsearch
[2024-01-24 12:06:53,805] [INFO] Running command: hmmsearch --tblout GCF_014269035.2_ASM1426903v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference/reference_markers.hmm GCF_014269035.2_ASM1426903v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:54,109] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:54,110] [INFO] Found 6/6 markers.
[2024-01-24 12:06:54,154] [INFO] Query marker FASTA was written to GCF_014269035.2_ASM1426903v2_genomic.fna/markers.fasta
[2024-01-24 12:06:54,154] [INFO] Task started: Blastn
[2024-01-24 12:06:54,154] [INFO] Running command: blastn -query GCF_014269035.2_ASM1426903v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference/reference_markers.fasta -out GCF_014269035.2_ASM1426903v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:55,205] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:55,212] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:55,213] [INFO] Target genome list was writen to GCF_014269035.2_ASM1426903v2_genomic.fna/target_genomes.txt
[2024-01-24 12:06:55,218] [INFO] Task started: fastANI
[2024-01-24 12:06:55,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg841e3e21-c9d3-47c3-b157-0e14cb1f9ac7/GCF_014269035.2_ASM1426903v2_genomic.fna.gz --refList GCF_014269035.2_ASM1426903v2_genomic.fna/target_genomes.txt --output GCF_014269035.2_ASM1426903v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:14,262] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:14,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:14,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:14,275] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:14,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:14,275] [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 urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	98.4309	1651	1849	95	conclusive
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	98.4214	1695	1849	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	88.6215	1404	1849	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	88.5529	1339	1849	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	87.9991	1333	1849	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	87.9785	1340	1849	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	87.6821	1430	1849	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	87.2544	1389	1849	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	87.2502	1338	1849	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	87.2403	1370	1849	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	86.9669	1386	1849	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.9304	1278	1849	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	86.532	1328	1849	95	below_threshold
Pseudomonas juntendi	strain=BML3	GCA_009932375.1	2666183	2666183	type	True	86.3633	1202	1849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:14,277] [INFO] DFAST Taxonomy check result was written to GCF_014269035.2_ASM1426903v2_genomic.fna/tc_result.tsv
[2024-01-24 12:07:14,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:14,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:14,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference/checkm_data
[2024-01-24 12:07:14,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:14,335] [INFO] Task started: CheckM
[2024-01-24 12:07:14,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014269035.2_ASM1426903v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014269035.2_ASM1426903v2_genomic.fna/checkm_input GCF_014269035.2_ASM1426903v2_genomic.fna/checkm_result
[2024-01-24 12:08:11,538] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:11,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:11,567] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:11,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:11,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014269035.2_ASM1426903v2_genomic.fna/markers.fasta)
[2024-01-24 12:08:11,568] [INFO] Task started: Blastn
[2024-01-24 12:08:11,568] [INFO] Running command: blastn -query GCF_014269035.2_ASM1426903v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8872bff4-d8bd-427b-b107-23b8c5801530/dqc_reference/reference_markers_gtdb.fasta -out GCF_014269035.2_ASM1426903v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:13,485] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:13,489] [INFO] Selected 11 target genomes.
[2024-01-24 12:08:13,489] [INFO] Target genome list was writen to GCF_014269035.2_ASM1426903v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:13,501] [INFO] Task started: fastANI
[2024-01-24 12:08:13,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg841e3e21-c9d3-47c3-b157-0e14cb1f9ac7/GCF_014269035.2_ASM1426903v2_genomic.fna.gz --refList GCF_014269035.2_ASM1426903v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014269035.2_ASM1426903v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:30,410] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:30,426] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:30,427] [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
GCA_003428805.1	s__Pseudomonas_E sp003428805	96.1004	1620	1849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	conclusive
GCF_009391885.1	s__Pseudomonas_E sp009391885	93.0533	1580	1849	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_017744435.1	s__Pseudomonas_E sp017744435	92.3074	1503	1849	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_003097235.1	s__Pseudomonas_E sp003097235	92.3053	1593	1849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009883635.2	s__Pseudomonas_E putida_W	91.9224	1589	1849	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_002906855.1	s__Pseudomonas_E putida_N	91.8755	1545	1849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	91.8685	1605	1849	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_001320245.1	s__Pseudomonas_E sp001320245	91.4559	1540	1849	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_002025705.1	s__Pseudomonas_E putida_J	91.2957	1554	1849	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_002165135.1	s__Pseudomonas_E sp002165135	87.7639	1360	1849	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_015680405.1	s__Pseudomonas_E pudica	87.6057	1404	1849	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:30,428] [INFO] GTDB search result was written to GCF_014269035.2_ASM1426903v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:30,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:30,432] [INFO] DFAST_QC result json was written to GCF_014269035.2_ASM1426903v2_genomic.fna/dqc_result.json
[2024-01-24 12:08:30,432] [INFO] DFAST_QC completed!
[2024-01-24 12:08:30,432] [INFO] Total running time: 0h1m57s