[2024-01-24 10:57:26,545] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference
[2024-01-24 10:57:27,852] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,853] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,853] [INFO] Running command: gunzip -c /var/lib/cwl/stg47571893-07e2-4b8f-a387-3a6afa8f59b5/GCF_018968705.1_ASM1896870v1_genomic.fna.gz | prodigal -d GCF_018968705.1_ASM1896870v1_genomic.fna/cds.fna -a GCF_018968705.1_ASM1896870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:51,281] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:51,281] [INFO] Task started: HMMsearch
[2024-01-24 10:57:51,281] [INFO] Running command: hmmsearch --tblout GCF_018968705.1_ASM1896870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference/reference_markers.hmm GCF_018968705.1_ASM1896870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:51,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:51,607] [INFO] Found 6/6 markers.
[2024-01-24 10:57:51,654] [INFO] Query marker FASTA was written to GCF_018968705.1_ASM1896870v1_genomic.fna/markers.fasta
[2024-01-24 10:57:51,654] [INFO] Task started: Blastn
[2024-01-24 10:57:51,654] [INFO] Running command: blastn -query GCF_018968705.1_ASM1896870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference/reference_markers.fasta -out GCF_018968705.1_ASM1896870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:52,641] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:52,644] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:52,645] [INFO] Target genome list was writen to GCF_018968705.1_ASM1896870v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:52,665] [INFO] Task started: fastANI
[2024-01-24 10:57:52,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg47571893-07e2-4b8f-a387-3a6afa8f59b5/GCF_018968705.1_ASM1896870v1_genomic.fna.gz --refList GCF_018968705.1_ASM1896870v1_genomic.fna/target_genomes.txt --output GCF_018968705.1_ASM1896870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:17,868] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:17,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:17,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:17,883] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:17,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:17,884] [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 cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	94.5203	1726	1956	95	below_threshold
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	94.5086	1764	1956	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	94.5008	1732	1956	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	83.4595	1168	1956	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	83.2879	1235	1956	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	83.2516	1201	1956	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	83.0591	1183	1956	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	83.0535	927	1956	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	82.9276	1240	1956	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	82.9212	1179	1956	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	82.8285	1163	1956	95	below_threshold
Pseudomonas ficuserectae	strain=ICMP7848	GCA_001400815.1	53410	53410	type	True	82.5851	1046	1956	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	80.9373	917	1956	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	80.7243	842	1956	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	80.3366	734	1956	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	80.2238	805	1956	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	80.164	754	1956	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	79.9093	716	1956	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	79.8346	588	1956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,886] [INFO] DFAST Taxonomy check result was written to GCF_018968705.1_ASM1896870v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:17,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:17,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:17,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference/checkm_data
[2024-01-24 10:58:17,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:17,944] [INFO] Task started: CheckM
[2024-01-24 10:58:17,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018968705.1_ASM1896870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018968705.1_ASM1896870v1_genomic.fna/checkm_input GCF_018968705.1_ASM1896870v1_genomic.fna/checkm_result
[2024-01-24 10:59:33,628] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:33,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:33,649] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:33,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:33,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018968705.1_ASM1896870v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:33,650] [INFO] Task started: Blastn
[2024-01-24 10:59:33,650] [INFO] Running command: blastn -query GCF_018968705.1_ASM1896870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5cf1359-6f9c-4431-95fe-5b5e059eed3c/dqc_reference/reference_markers_gtdb.fasta -out GCF_018968705.1_ASM1896870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:35,262] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:35,265] [INFO] Selected 5 target genomes.
[2024-01-24 10:59:35,265] [INFO] Target genome list was writen to GCF_018968705.1_ASM1896870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:35,268] [INFO] Task started: fastANI
[2024-01-24 10:59:35,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg47571893-07e2-4b8f-a387-3a6afa8f59b5/GCF_018968705.1_ASM1896870v1_genomic.fna.gz --refList GCF_018968705.1_ASM1896870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018968705.1_ASM1896870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:43,624] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:43,629] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:43,630] [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_018968705.1	s__Pseudomonas_E cichorii_C	100.0	1956	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.11	0.91	0.89	3	conclusive
GCF_018343775.1	s__Pseudomonas_E cichorii	94.5097	1765	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.65	99.06	0.98	0.95	8	-
GCF_017165745.1	s__Pseudomonas_E capsici	92.6331	1722	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	97.35	0.95	0.93	13	-
GCF_015471405.1	s__Pseudomonas_E cichorii_D	90.4149	1682	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.41	0.90	0.90	2	-
GCF_003700275.1	s__Pseudomonas_E cichorii_B	87.8907	1621	1956	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 10:59:43,631] [INFO] GTDB search result was written to GCF_018968705.1_ASM1896870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:43,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:43,635] [INFO] DFAST_QC result json was written to GCF_018968705.1_ASM1896870v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:43,635] [INFO] DFAST_QC completed!
[2024-01-24 10:59:43,635] [INFO] Total running time: 0h2m17s