[2024-01-24 14:20:00,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:00,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:00,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference
[2024-01-24 14:20:02,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,168] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg951f654d-3497-4f74-8343-e55c2114f2bc/GCF_012986245.1_ASM1298624v1_genomic.fna.gz | prodigal -d GCF_012986245.1_ASM1298624v1_genomic.fna/cds.fna -a GCF_012986245.1_ASM1298624v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:21,787] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:21,788] [INFO] Task started: HMMsearch
[2024-01-24 14:20:21,788] [INFO] Running command: hmmsearch --tblout GCF_012986245.1_ASM1298624v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference/reference_markers.hmm GCF_012986245.1_ASM1298624v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:22,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:22,098] [INFO] Found 6/6 markers.
[2024-01-24 14:20:22,145] [INFO] Query marker FASTA was written to GCF_012986245.1_ASM1298624v1_genomic.fna/markers.fasta
[2024-01-24 14:20:22,146] [INFO] Task started: Blastn
[2024-01-24 14:20:22,146] [INFO] Running command: blastn -query GCF_012986245.1_ASM1298624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference/reference_markers.fasta -out GCF_012986245.1_ASM1298624v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:23,228] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:23,231] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:23,231] [INFO] Target genome list was writen to GCF_012986245.1_ASM1298624v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:23,237] [INFO] Task started: fastANI
[2024-01-24 14:20:23,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg951f654d-3497-4f74-8343-e55c2114f2bc/GCF_012986245.1_ASM1298624v1_genomic.fna.gz --refList GCF_012986245.1_ASM1298624v1_genomic.fna/target_genomes.txt --output GCF_012986245.1_ASM1298624v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:45,835] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:45,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:45,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:45,855] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:45,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:45,856] [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 nitroreducens	strain=DSM 14399	GCA_012986245.1	46680	46680	suspected-type	True	100.0	2042	2043	95	conclusive
Pseudomonas nitroreducens	strain=NBRC 12694	GCA_002091755.1	46680	46680	suspected-type	True	99.986	2013	2043	95	conclusive
Pseudomonas nicosulfuronedens	strain=LAM1902	GCA_005877905.1	2571105	2571105	type	True	91.7362	1804	2043	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	86.6196	1511	2043	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	86.6047	1485	2043	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	86.5801	1523	2043	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	86.5373	1503	2043	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	85.9929	1418	2043	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	85.5842	1254	2043	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	85.5467	1264	2043	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	83.6034	1255	2043	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	83.5761	1273	2043	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.3203	913	2043	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.0434	984	2043	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.9439	996	2043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:45,858] [INFO] DFAST Taxonomy check result was written to GCF_012986245.1_ASM1298624v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:45,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:45,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:45,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference/checkm_data
[2024-01-24 14:20:45,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:45,925] [INFO] Task started: CheckM
[2024-01-24 14:20:45,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012986245.1_ASM1298624v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012986245.1_ASM1298624v1_genomic.fna/checkm_input GCF_012986245.1_ASM1298624v1_genomic.fna/checkm_result
[2024-01-24 14:21:44,344] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:44,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:44,365] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:44,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:44,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012986245.1_ASM1298624v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:44,366] [INFO] Task started: Blastn
[2024-01-24 14:21:44,366] [INFO] Running command: blastn -query GCF_012986245.1_ASM1298624v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a0073f6-7404-4b34-9e2e-1a2c6af2d9a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_012986245.1_ASM1298624v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:46,439] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:46,443] [INFO] Selected 13 target genomes.
[2024-01-24 14:21:46,444] [INFO] Target genome list was writen to GCF_012986245.1_ASM1298624v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:46,470] [INFO] Task started: fastANI
[2024-01-24 14:21:46,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg951f654d-3497-4f74-8343-e55c2114f2bc/GCF_012986245.1_ASM1298624v1_genomic.fna.gz --refList GCF_012986245.1_ASM1298624v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012986245.1_ASM1298624v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:07,967] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:07,983] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:07,983] [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_002091755.1	s__Pseudomonas nitroreducens	99.986	2013	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	98.47	95.19	0.93	0.83	16	conclusive
GCF_000955805.1	s__Pseudomonas sp000955805	93.262	1804	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.94	99.94	0.99	0.99	2	-
GCF_008807415.1	s__Pseudomonas sp002079985	91.8413	1825	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	97.48	95.53	0.92	0.91	9	-
GCF_005877905.1	s__Pseudomonas nicosulfuronedens	91.7361	1804	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919445.1	s__Pseudomonas sp016919445	91.6878	1762	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014852585.1	s__Pseudomonas sp014852585	91.458	1806	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	91.2502	1504	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796985.1	s__Pseudomonas sp002796985	91.2391	1673	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204515.1	s__Pseudomonas nitritireducens_A	91.1915	1795	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313755.1	s__Pseudomonas nitroreducens_A	91.188	1706	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	96.60	96.60	0.86	0.86	2	-
GCF_000349845.1	s__Pseudomonas sp000349845	89.6149	1514	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	89.5598	1564	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009189165.1	s__Pseudomonas sp009189165	89.1469	1566	2043	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:07,985] [INFO] GTDB search result was written to GCF_012986245.1_ASM1298624v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:07,985] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:07,989] [INFO] DFAST_QC result json was written to GCF_012986245.1_ASM1298624v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:07,989] [INFO] DFAST_QC completed!
[2024-01-24 14:22:07,989] [INFO] Total running time: 0h2m7s