[2024-01-24 12:16:08,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference
[2024-01-24 12:16:10,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:10,005] [INFO] Task started: Prodigal
[2024-01-24 12:16:10,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ed2762f-161d-4908-b62d-0c3bf1f0bb44/GCF_001400175.1_PcbICMP2823_genomic.fna.gz | prodigal -d GCF_001400175.1_PcbICMP2823_genomic.fna/cds.fna -a GCF_001400175.1_PcbICMP2823_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:26,108] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:26,109] [INFO] Task started: HMMsearch
[2024-01-24 12:16:26,109] [INFO] Running command: hmmsearch --tblout GCF_001400175.1_PcbICMP2823_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference/reference_markers.hmm GCF_001400175.1_PcbICMP2823_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:26,451] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:26,453] [INFO] Found 6/6 markers.
[2024-01-24 12:16:26,505] [INFO] Query marker FASTA was written to GCF_001400175.1_PcbICMP2823_genomic.fna/markers.fasta
[2024-01-24 12:16:26,506] [INFO] Task started: Blastn
[2024-01-24 12:16:26,506] [INFO] Running command: blastn -query GCF_001400175.1_PcbICMP2823_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference/reference_markers.fasta -out GCF_001400175.1_PcbICMP2823_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:27,427] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:27,431] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:27,431] [INFO] Target genome list was writen to GCF_001400175.1_PcbICMP2823_genomic.fna/target_genomes.txt
[2024-01-24 12:16:27,457] [INFO] Task started: fastANI
[2024-01-24 12:16:27,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed2762f-161d-4908-b62d-0c3bf1f0bb44/GCF_001400175.1_PcbICMP2823_genomic.fna.gz --refList GCF_001400175.1_PcbICMP2823_genomic.fna/target_genomes.txt --output GCF_001400175.1_PcbICMP2823_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:52,982] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:52,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:52,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:53,005] [INFO] Found 20 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:16:53,005] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:53,005] [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 cannabina	strain=ICMP2823	GCA_001400175.1	86840	86840	type	True	100.0	1691	1708	95	conclusive
Pseudomonas cannabina	strain=ICMP 2823	GCA_900100365.1	86840	86840	type	True	99.9815	1702	1708	95	conclusive
Pseudomonas cannabina	strain=ICMP 15200	GCA_001401375.1	86840	86840	pathovar	True	97.7021	1515	1708	95	conclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	87.7501	1407	1708	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	87.6567	1365	1708	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	87.6162	1420	1708	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP 2844	GCA_001401135.1	251701	251701	pathovar	True	87.6144	1371	1708	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4303	GCA_001401395.1	251701	251701	pathovar	True	87.5058	1355	1708	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	87.4229	1380	1708	95	below_threshold
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	87.3998	1199	1708	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	86.4449	1382	1708	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	86.387	1345	1708	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	86.1215	1079	1708	95	below_threshold
Pseudomonas syringae	strain=ICMP3023	GCA_001401075.1	317	317	suspected-type	True	86.1072	1344	1708	95	below_threshold
Pseudomonas syringae	strain=KCTC 12500	GCA_000507185.2	317	317	suspected-type	True	86.024	1394	1708	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	85.7407	1396	1708	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	85.6417	1374	1708	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	80.1136	681	1708	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	80.0909	700	1708	95	below_threshold
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	76.9304	236	1708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:53,008] [INFO] DFAST Taxonomy check result was written to GCF_001400175.1_PcbICMP2823_genomic.fna/tc_result.tsv
[2024-01-24 12:16:53,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:53,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:53,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference/checkm_data
[2024-01-24 12:16:53,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:53,070] [INFO] Task started: CheckM
[2024-01-24 12:16:53,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001400175.1_PcbICMP2823_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001400175.1_PcbICMP2823_genomic.fna/checkm_input GCF_001400175.1_PcbICMP2823_genomic.fna/checkm_result
[2024-01-24 12:17:42,032] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:42,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:42,057] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:42,057] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:42,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001400175.1_PcbICMP2823_genomic.fna/markers.fasta)
[2024-01-24 12:17:42,058] [INFO] Task started: Blastn
[2024-01-24 12:17:42,058] [INFO] Running command: blastn -query GCF_001400175.1_PcbICMP2823_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e528c3d-be8e-4f03-ac58-72ce152c402e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001400175.1_PcbICMP2823_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:43,642] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:43,646] [INFO] Selected 9 target genomes.
[2024-01-24 12:17:43,647] [INFO] Target genome list was writen to GCF_001400175.1_PcbICMP2823_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:43,654] [INFO] Task started: fastANI
[2024-01-24 12:17:43,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed2762f-161d-4908-b62d-0c3bf1f0bb44/GCF_001400175.1_PcbICMP2823_genomic.fna.gz --refList GCF_001400175.1_PcbICMP2823_genomic.fna/target_genomes_gtdb.txt --output GCF_001400175.1_PcbICMP2823_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:57,224] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:57,240] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 12:17:57,240] [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_900100365.1	s__Pseudomonas_E cannabina	99.9815	1702	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.50	95.44	0.90	0.84	17	inconclusive
GCF_001293775.1	s__Pseudomonas_E syringae_P	95.049	1538	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	inconclusive
GCF_001466965.1	s__Pseudomonas_E syringae_Q	89.7644	1391	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.87	0.94	0.94	3	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	89.1614	1388	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
GCF_000444135.1	s__Pseudomonas_E avellanae	87.6681	1282	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	-
GCF_009176725.1	s__Pseudomonas_E syringae_M	86.4316	1377	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	98.71	98.38	0.92	0.88	59	-
GCF_001401155.1	s__Pseudomonas_E tremae	86.1836	1323	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.42	0.92	0.88	76	-
GCF_000507185.2	s__Pseudomonas_E syringae	86.0257	1394	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	97.83	96.00	0.92	0.85	147	-
GCF_001400735.1	s__Pseudomonas_E caricapapayae	85.5927	1369	1708	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	97.41	0.91	0.88	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:57,243] [INFO] GTDB search result was written to GCF_001400175.1_PcbICMP2823_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:57,243] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:57,248] [INFO] DFAST_QC result json was written to GCF_001400175.1_PcbICMP2823_genomic.fna/dqc_result.json
[2024-01-24 12:17:57,248] [INFO] DFAST_QC completed!
[2024-01-24 12:17:57,249] [INFO] Total running time: 0h1m49s