[2024-01-24 14:14:37,355] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,359] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference
[2024-01-24 14:14:38,850] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,853] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgd78ea4d5-8d57-4ea4-a0d1-3b59bde2c28c/GCF_014269025.2_ASM1426902v2_genomic.fna.gz | prodigal -d GCF_014269025.2_ASM1426902v2_genomic.fna/cds.fna -a GCF_014269025.2_ASM1426902v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:02,201] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:02,201] [INFO] Task started: HMMsearch
[2024-01-24 14:15:02,201] [INFO] Running command: hmmsearch --tblout GCF_014269025.2_ASM1426902v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference/reference_markers.hmm GCF_014269025.2_ASM1426902v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:02,538] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:02,539] [INFO] Found 6/6 markers.
[2024-01-24 14:15:02,581] [INFO] Query marker FASTA was written to GCF_014269025.2_ASM1426902v2_genomic.fna/markers.fasta
[2024-01-24 14:15:02,582] [INFO] Task started: Blastn
[2024-01-24 14:15:02,582] [INFO] Running command: blastn -query GCF_014269025.2_ASM1426902v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference/reference_markers.fasta -out GCF_014269025.2_ASM1426902v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:03,664] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:03,667] [INFO] Selected 18 target genomes.
[2024-01-24 14:15:03,668] [INFO] Target genome list was writen to GCF_014269025.2_ASM1426902v2_genomic.fna/target_genomes.txt
[2024-01-24 14:15:03,675] [INFO] Task started: fastANI
[2024-01-24 14:15:03,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78ea4d5-8d57-4ea4-a0d1-3b59bde2c28c/GCF_014269025.2_ASM1426902v2_genomic.fna.gz --refList GCF_014269025.2_ASM1426902v2_genomic.fna/target_genomes.txt --output GCF_014269025.2_ASM1426902v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:25,908] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:25,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:25,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:25,929] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:25,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:25,929] [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	86.9662	1318	1682	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.9584	1369	1682	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	86.1842	1171	1682	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	86.1016	1251	1682	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	85.6293	1178	1682	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	85.5624	1183	1682	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	85.5159	1230	1682	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	85.3397	1177	1682	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	85.3193	1216	1682	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	85.1974	1213	1682	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	85.1497	1210	1682	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	85.0102	1225	1682	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	84.9291	1126	1682	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	84.6756	1180	1682	95	below_threshold
Pseudomonas parafulva	strain=NBRC 16636	GCA_000730645.1	157782	157782	suspected-type	True	83.7719	1104	1682	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	83.7218	1118	1682	95	below_threshold
Pseudomonas fulva	strain=DSM 17717	GCA_000621265.1	47880	47880	type	True	82.9425	1041	1682	95	below_threshold
Pseudomonas fulva	strain=NBRC 16637	GCA_000730565.1	47880	47880	type	True	82.8824	1037	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:25,931] [INFO] DFAST Taxonomy check result was written to GCF_014269025.2_ASM1426902v2_genomic.fna/tc_result.tsv
[2024-01-24 14:15:25,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:25,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:25,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference/checkm_data
[2024-01-24 14:15:25,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:25,988] [INFO] Task started: CheckM
[2024-01-24 14:15:25,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014269025.2_ASM1426902v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014269025.2_ASM1426902v2_genomic.fna/checkm_input GCF_014269025.2_ASM1426902v2_genomic.fna/checkm_result
[2024-01-24 14:16:32,500] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:32,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:32,529] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:32,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:32,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014269025.2_ASM1426902v2_genomic.fna/markers.fasta)
[2024-01-24 14:16:32,531] [INFO] Task started: Blastn
[2024-01-24 14:16:32,531] [INFO] Running command: blastn -query GCF_014269025.2_ASM1426902v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg552087ba-16d7-4e38-b44f-d3f20716ba0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014269025.2_ASM1426902v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:37,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:37,134] [INFO] Selected 12 target genomes.
[2024-01-24 14:16:37,134] [INFO] Target genome list was writen to GCF_014269025.2_ASM1426902v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:37,164] [INFO] Task started: fastANI
[2024-01-24 14:16:37,164] [INFO] Running command: fastANI --query /var/lib/cwl/stgd78ea4d5-8d57-4ea4-a0d1-3b59bde2c28c/GCF_014269025.2_ASM1426902v2_genomic.fna.gz --refList GCF_014269025.2_ASM1426902v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014269025.2_ASM1426902v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:54,874] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:54,931] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:54,931] [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_014269025.2	s__Pseudomonas_E monteilii_C	100.0	1680	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.83	98.50	0.90	0.88	3	conclusive
GCF_002112505.1	s__Pseudomonas_E sp002112505	87.8216	1361	1682	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	87.727	1359	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.29	96.26	0.90	0.90	5	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	87.5903	1312	1682	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	87.451	1355	1682	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	87.274	1387	1682	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	87.2374	1337	1682	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_001320245.1	s__Pseudomonas_E sp001320245	87.0705	1317	1682	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_003428805.1	s__Pseudomonas_E sp003428805	86.9863	1361	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	85.5601	1190	1682	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_002113165.1	s__Pseudomonas_E sp002113165	85.4209	1214	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015680405.1	s__Pseudomonas_E pudica	85.3729	1204	1682	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 14:16:54,933] [INFO] GTDB search result was written to GCF_014269025.2_ASM1426902v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:54,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:54,937] [INFO] DFAST_QC result json was written to GCF_014269025.2_ASM1426902v2_genomic.fna/dqc_result.json
[2024-01-24 14:16:54,938] [INFO] DFAST_QC completed!
[2024-01-24 14:16:54,938] [INFO] Total running time: 0h2m18s