[2024-01-24 13:09:49,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,076] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference
[2024-01-24 13:09:50,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,384] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg20a2ad18-6b34-4edd-9d65-d6a4c417b4b5/GCF_021602465.1_ASM2160246v1_genomic.fna.gz | prodigal -d GCF_021602465.1_ASM2160246v1_genomic.fna/cds.fna -a GCF_021602465.1_ASM2160246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:10,285] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:10,286] [INFO] Task started: HMMsearch
[2024-01-24 13:10:10,286] [INFO] Running command: hmmsearch --tblout GCF_021602465.1_ASM2160246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference/reference_markers.hmm GCF_021602465.1_ASM2160246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:10,587] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:10,588] [INFO] Found 6/6 markers.
[2024-01-24 13:10:10,636] [INFO] Query marker FASTA was written to GCF_021602465.1_ASM2160246v1_genomic.fna/markers.fasta
[2024-01-24 13:10:10,637] [INFO] Task started: Blastn
[2024-01-24 13:10:10,637] [INFO] Running command: blastn -query GCF_021602465.1_ASM2160246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference/reference_markers.fasta -out GCF_021602465.1_ASM2160246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:11,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:11,612] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:11,612] [INFO] Target genome list was writen to GCF_021602465.1_ASM2160246v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:11,686] [INFO] Task started: fastANI
[2024-01-24 13:10:11,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a2ad18-6b34-4edd-9d65-d6a4c417b4b5/GCF_021602465.1_ASM2160246v1_genomic.fna.gz --refList GCF_021602465.1_ASM2160246v1_genomic.fna/target_genomes.txt --output GCF_021602465.1_ASM2160246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:31,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:31,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:31,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:31,707] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:31,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:31,707] [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_021602465.1	2740517	2740517	suspected-type	True	100.0	1952	1955	95	conclusive
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	99.9695	1883	1955	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	88.6539	1432	1955	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	88.6161	1348	1955	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	87.9753	1322	1955	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	87.9173	1374	1955	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	87.8866	1453	1955	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	87.4094	1408	1955	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	87.3708	1391	1955	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	87.1813	1407	1955	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.9404	1281	1955	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	86.849	1395	1955	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	86.5011	1331	1955	95	below_threshold
Pseudomonas juntendi	strain=BML3	GCA_009932375.1	2666183	2666183	type	True	86.4565	1200	1955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:31,714] [INFO] DFAST Taxonomy check result was written to GCF_021602465.1_ASM2160246v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:31,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:31,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:31,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference/checkm_data
[2024-01-24 13:10:31,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:31,775] [INFO] Task started: CheckM
[2024-01-24 13:10:31,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021602465.1_ASM2160246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021602465.1_ASM2160246v1_genomic.fna/checkm_input GCF_021602465.1_ASM2160246v1_genomic.fna/checkm_result
[2024-01-24 13:11:30,443] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:30,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:30,466] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:30,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:30,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021602465.1_ASM2160246v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:30,467] [INFO] Task started: Blastn
[2024-01-24 13:11:30,467] [INFO] Running command: blastn -query GCF_021602465.1_ASM2160246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7407aeca-f3f1-4467-9f6b-40044f2366fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_021602465.1_ASM2160246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:32,041] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:32,045] [INFO] Selected 15 target genomes.
[2024-01-24 13:11:32,046] [INFO] Target genome list was writen to GCF_021602465.1_ASM2160246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:32,842] [INFO] Task started: fastANI
[2024-01-24 13:11:32,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a2ad18-6b34-4edd-9d65-d6a4c417b4b5/GCF_021602465.1_ASM2160246v1_genomic.fna.gz --refList GCF_021602465.1_ASM2160246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021602465.1_ASM2160246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:56,151] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:56,180] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:56,181] [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	96.045	1656	1955	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	93.1555	1595	1955	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	92.4074	1585	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	92.2829	1520	1955	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	91.9454	1582	1955	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_009883635.2	s__Pseudomonas_E putida_W	91.8542	1596	1955	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_002112505.1	s__Pseudomonas_E sp002112505	91.7428	1624	1955	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	91.5326	1601	1955	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	91.1921	1591	1955	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	87.7374	1359	1955	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	87.5821	1431	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_009932375.1	s__Pseudomonas_E juntendi	86.4382	1201	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_007677725.1	s__Pseudomonas_E sp003445295	86.1768	1331	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	98.48	0.95	0.95	2	-
GCF_900589395.1	s__Pseudomonas_E sp900589395	81.1431	923	1955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.16	0.94	0.93	8	-
GCF_003208475.1	s__Pseudomonas_E sp003208475	80.6613	876	1955	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 13:11:56,183] [INFO] GTDB search result was written to GCF_021602465.1_ASM2160246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:56,183] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:56,188] [INFO] DFAST_QC result json was written to GCF_021602465.1_ASM2160246v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:56,189] [INFO] DFAST_QC completed!
[2024-01-24 13:11:56,189] [INFO] Total running time: 0h2m7s