[2024-01-24 11:34:55,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,267] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference
[2024-01-24 11:34:56,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,759] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg23b79dba-9551-4dd1-95f9-e7bc5baa54f7/GCF_001401075.1_PsyICMP3023_genomic.fna.gz | prodigal -d GCF_001401075.1_PsyICMP3023_genomic.fna/cds.fna -a GCF_001401075.1_PsyICMP3023_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:18,587] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:18,587] [INFO] Task started: HMMsearch
[2024-01-24 11:35:18,587] [INFO] Running command: hmmsearch --tblout GCF_001401075.1_PsyICMP3023_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference/reference_markers.hmm GCF_001401075.1_PsyICMP3023_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:18,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:18,933] [INFO] Found 6/6 markers.
[2024-01-24 11:35:18,982] [INFO] Query marker FASTA was written to GCF_001401075.1_PsyICMP3023_genomic.fna/markers.fasta
[2024-01-24 11:35:18,982] [INFO] Task started: Blastn
[2024-01-24 11:35:18,982] [INFO] Running command: blastn -query GCF_001401075.1_PsyICMP3023_genomic.fna/markers.fasta -db /var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference/reference_markers.fasta -out GCF_001401075.1_PsyICMP3023_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:19,960] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:19,964] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:19,964] [INFO] Target genome list was writen to GCF_001401075.1_PsyICMP3023_genomic.fna/target_genomes.txt
[2024-01-24 11:35:19,969] [INFO] Task started: fastANI
[2024-01-24 11:35:19,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b79dba-9551-4dd1-95f9-e7bc5baa54f7/GCF_001401075.1_PsyICMP3023_genomic.fna.gz --refList GCF_001401075.1_PsyICMP3023_genomic.fna/target_genomes.txt --output GCF_001401075.1_PsyICMP3023_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:35,719] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:35,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:35,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:35,730] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {}, {317: 'Pseudomonas syringae', 251699: 'Pseudomonas syringae group genomosp. 7', 251701: 'Pseudomonas syringae group genomosp. 3'}
[2024-01-24 11:35:35,730] [INFO] Found 11 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:35:35,731] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:35,731] [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 syringae	strain=ICMP3023	GCA_001401075.1	317	317	suspected-type	True	100.0	1931	1941	95	inconclusive
Pseudomonas syringae	strain=KCTC 12500	GCA_000507185.2	317	317	suspected-type	True	99.9971	1941	1941	95	inconclusive
Pseudomonas syringae	strain=DSM 10604	GCA_000597765.1	317	317	suspected-type	True	99.9862	1923	1941	95	inconclusive
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	96.2961	1632	1941	95	inconclusive
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	96.0217	1259	1941	95	inconclusive
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	89.2836	1527	1941	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	88.4221	1559	1941	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	88.3488	1558	1941	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	86.9218	1434	1941	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	80.0973	697	1941	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	79.8402	683	1941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:35,733] [INFO] DFAST Taxonomy check result was written to GCF_001401075.1_PsyICMP3023_genomic.fna/tc_result.tsv
[2024-01-24 11:35:35,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:35,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:35,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference/checkm_data
[2024-01-24 11:35:35,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:35,794] [INFO] Task started: CheckM
[2024-01-24 11:35:35,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001401075.1_PsyICMP3023_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001401075.1_PsyICMP3023_genomic.fna/checkm_input GCF_001401075.1_PsyICMP3023_genomic.fna/checkm_result
[2024-01-24 11:36:39,982] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:39,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:40,006] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:40,006] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:40,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001401075.1_PsyICMP3023_genomic.fna/markers.fasta)
[2024-01-24 11:36:40,007] [INFO] Task started: Blastn
[2024-01-24 11:36:40,007] [INFO] Running command: blastn -query GCF_001401075.1_PsyICMP3023_genomic.fna/markers.fasta -db /var/lib/cwl/stg5df88b50-bad9-4516-a64d-614fa4409ffd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001401075.1_PsyICMP3023_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:41,701] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:41,706] [INFO] Selected 9 target genomes.
[2024-01-24 11:36:41,706] [INFO] Target genome list was writen to GCF_001401075.1_PsyICMP3023_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:41,714] [INFO] Task started: fastANI
[2024-01-24 11:36:41,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b79dba-9551-4dd1-95f9-e7bc5baa54f7/GCF_001401075.1_PsyICMP3023_genomic.fna.gz --refList GCF_001401075.1_PsyICMP3023_genomic.fna/target_genomes_gtdb.txt --output GCF_001401075.1_PsyICMP3023_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:57,307] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:57,320] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:57,320] [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_000507185.2	s__Pseudomonas_E syringae	99.9971	1941	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	97.83	96.00	0.92	0.85	147	conclusive
GCF_009176725.1	s__Pseudomonas_E syringae_M	95.0541	1738	1941	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_900074915.1	s__Pseudomonas_E cerasi	94.454	1648	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.51	98.33	0.88	0.83	51	-
GCF_900103225.1	s__Pseudomonas_E congelans	94.2349	1652	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.60	98.04	0.95	0.92	20	-
GCF_002699855.1	s__Pseudomonas_E amygdali	89.3915	1426	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	96.47	0.89	0.82	226	-
GCF_001400735.1	s__Pseudomonas_E caricapapayae	88.3536	1553	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	97.41	0.91	0.88	11	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	86.4811	1525	1941	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_900100365.1	s__Pseudomonas_E cannabina	86.073	1465	1941	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.50	95.44	0.90	0.84	17	-
GCF_002087235.1	s__Pseudomonas_E floridensis	84.0833	1279	1941	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 11:36:57,322] [INFO] GTDB search result was written to GCF_001401075.1_PsyICMP3023_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:57,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:57,325] [INFO] DFAST_QC result json was written to GCF_001401075.1_PsyICMP3023_genomic.fna/dqc_result.json
[2024-01-24 11:36:57,325] [INFO] DFAST_QC completed!
[2024-01-24 11:36:57,325] [INFO] Total running time: 0h2m2s