[2024-01-25 17:58:50,456] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:50,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:50,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference
[2024-01-25 17:58:51,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:51,560] [INFO] Task started: Prodigal
[2024-01-25 17:58:51,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg862a3ebe-e3b0-485f-a49f-3bf720645ae7/GCF_017165765.1_ASM1716576v1_genomic.fna.gz | prodigal -d GCF_017165765.1_ASM1716576v1_genomic.fna/cds.fna -a GCF_017165765.1_ASM1716576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:59:08,351] [INFO] Task succeeded: Prodigal
[2024-01-25 17:59:08,352] [INFO] Task started: HMMsearch
[2024-01-25 17:59:08,352] [INFO] Running command: hmmsearch --tblout GCF_017165765.1_ASM1716576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference/reference_markers.hmm GCF_017165765.1_ASM1716576v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:59:08,633] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:59:08,634] [INFO] Found 6/6 markers.
[2024-01-25 17:59:08,677] [INFO] Query marker FASTA was written to GCF_017165765.1_ASM1716576v1_genomic.fna/markers.fasta
[2024-01-25 17:59:08,677] [INFO] Task started: Blastn
[2024-01-25 17:59:08,677] [INFO] Running command: blastn -query GCF_017165765.1_ASM1716576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference/reference_markers.fasta -out GCF_017165765.1_ASM1716576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:09,636] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:09,639] [INFO] Selected 17 target genomes.
[2024-01-25 17:59:09,639] [INFO] Target genome list was writen to GCF_017165765.1_ASM1716576v1_genomic.fna/target_genomes.txt
[2024-01-25 17:59:09,657] [INFO] Task started: fastANI
[2024-01-25 17:59:09,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg862a3ebe-e3b0-485f-a49f-3bf720645ae7/GCF_017165765.1_ASM1716576v1_genomic.fna.gz --refList GCF_017165765.1_ASM1716576v1_genomic.fna/target_genomes.txt --output GCF_017165765.1_ASM1716576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:29,659] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:29,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:29,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:29,670] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:29,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:29,670] [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	92.0195	1705	1917	95	below_threshold
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	92.0188	1725	1917	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	92.0075	1712	1917	95	below_threshold
Pseudomonas viridiflava	strain=DSM 6694	GCA_001305955.1	33069	33069	type	True	83.2859	1177	1917	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3882	GCA_001400955.1	251701	251701	pathovar	True	83.1905	1180	1917	95	below_threshold
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	82.9871	991	1917	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	82.9135	1115	1917	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	82.9107	907	1917	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	82.8831	1168	1917	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	82.8577	1175	1917	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	82.8325	1131	1917	95	below_threshold
Pseudomonas syringae	strain=KCTC 12500	GCA_000507185.2	317	317	suspected-type	True	82.829	1163	1917	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	80.2025	775	1917	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	80.1989	809	1917	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	80.1665	761	1917	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	80.164	686	1917	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	80.0829	704	1917	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:29,672] [INFO] DFAST Taxonomy check result was written to GCF_017165765.1_ASM1716576v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:29,672] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:29,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:29,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference/checkm_data
[2024-01-25 17:59:29,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:29,730] [INFO] Task started: CheckM
[2024-01-25 17:59:29,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017165765.1_ASM1716576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017165765.1_ASM1716576v1_genomic.fna/checkm_input GCF_017165765.1_ASM1716576v1_genomic.fna/checkm_result
[2024-01-25 18:00:24,262] [INFO] Task succeeded: CheckM
[2024-01-25 18:00:24,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:00:24,285] [INFO] ===== Completeness check finished =====
[2024-01-25 18:00:24,285] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:00:24,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017165765.1_ASM1716576v1_genomic.fna/markers.fasta)
[2024-01-25 18:00:24,287] [INFO] Task started: Blastn
[2024-01-25 18:00:24,287] [INFO] Running command: blastn -query GCF_017165765.1_ASM1716576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e36cf8-b6d6-4afd-ba7e-e7074eba9c77/dqc_reference/reference_markers_gtdb.fasta -out GCF_017165765.1_ASM1716576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:26,076] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:26,079] [INFO] Selected 5 target genomes.
[2024-01-25 18:00:26,079] [INFO] Target genome list was writen to GCF_017165765.1_ASM1716576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:00:26,087] [INFO] Task started: fastANI
[2024-01-25 18:00:26,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg862a3ebe-e3b0-485f-a49f-3bf720645ae7/GCF_017165765.1_ASM1716576v1_genomic.fna.gz --refList GCF_017165765.1_ASM1716576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017165765.1_ASM1716576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:00:34,275] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:34,280] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:00:34,280] [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_017165745.1	s__Pseudomonas_E capsici	99.9973	1911	1917	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	97.35	0.95	0.93	13	conclusive
GCF_018968705.1	s__Pseudomonas_E cichorii_C	92.6724	1724	1917	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.11	0.91	0.89	3	-
GCF_018343775.1	s__Pseudomonas_E cichorii	92.0188	1725	1917	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_015471405.1	s__Pseudomonas_E cichorii_D	89.8989	1674	1917	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	87.8915	1620	1917	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:00:34,281] [INFO] GTDB search result was written to GCF_017165765.1_ASM1716576v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:00:34,281] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:00:34,284] [INFO] DFAST_QC result json was written to GCF_017165765.1_ASM1716576v1_genomic.fna/dqc_result.json
[2024-01-25 18:00:34,284] [INFO] DFAST_QC completed!
[2024-01-25 18:00:34,284] [INFO] Total running time: 0h1m44s