[2024-01-24 13:57:45,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:45,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:45,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference
[2024-01-24 13:57:46,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,454] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg72552eeb-c1aa-403e-a40d-c30692e7c23d/GCF_001401155.1_PtrICMP9151_genomic.fna.gz | prodigal -d GCF_001401155.1_PtrICMP9151_genomic.fna/cds.fna -a GCF_001401155.1_PtrICMP9151_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:04,794] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:04,795] [INFO] Task started: HMMsearch
[2024-01-24 13:58:04,795] [INFO] Running command: hmmsearch --tblout GCF_001401155.1_PtrICMP9151_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference/reference_markers.hmm GCF_001401155.1_PtrICMP9151_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:05,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:05,139] [INFO] Found 6/6 markers.
[2024-01-24 13:58:05,203] [INFO] Query marker FASTA was written to GCF_001401155.1_PtrICMP9151_genomic.fna/markers.fasta
[2024-01-24 13:58:05,204] [INFO] Task started: Blastn
[2024-01-24 13:58:05,204] [INFO] Running command: blastn -query GCF_001401155.1_PtrICMP9151_genomic.fna/markers.fasta -db /var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference/reference_markers.fasta -out GCF_001401155.1_PtrICMP9151_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:06,234] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:06,238] [INFO] Selected 25 target genomes.
[2024-01-24 13:58:06,239] [INFO] Target genome list was writen to GCF_001401155.1_PtrICMP9151_genomic.fna/target_genomes.txt
[2024-01-24 13:58:06,256] [INFO] Task started: fastANI
[2024-01-24 13:58:06,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg72552eeb-c1aa-403e-a40d-c30692e7c23d/GCF_001401155.1_PtrICMP9151_genomic.fna.gz --refList GCF_001401155.1_PtrICMP9151_genomic.fna/target_genomes.txt --output GCF_001401155.1_PtrICMP9151_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,094] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,113] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:36,113] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:36,114] [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 group genomosp. 3	strain=ICMP4116	GCA_001401405.1	251701	251701	pathovar	True	87.0185	1441	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP 2844	GCA_001401135.1	251701	251701	pathovar	True	86.8421	1428	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=DC3000	GCA_000007805.1	251701	251701	type	True	86.8113	1493	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP8903	GCA_001400595.1	251701	251701	pathovar	True	86.7664	1406	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	86.7096	1419	1864	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000444135.1	46257	46257	type	True	86.7065	1330	1864	95	below_threshold
Pseudomonas avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	86.6776	1393	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP2814	GCA_001401385.1	251701	251701	pathovar	True	86.6555	1416	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP4303	GCA_001401395.1	251701	251701	pathovar	True	86.6449	1420	1864	95	below_threshold
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	86.6275	1446	1864	95	below_threshold
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	86.5484	1459	1864	95	below_threshold
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	86.5477	1254	1864	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	86.5464	1383	1864	95	below_threshold
Pseudomonas cannabina	strain=ICMP 15200	GCA_001401375.1	86840	86840	pathovar	True	86.3574	1358	1864	95	below_threshold
Pseudomonas cannabina	strain=ICMP2823	GCA_001400175.1	86840	86840	type	True	86.1906	1311	1864	95	below_threshold
Pseudomonas cannabina	strain=ICMP 2823	GCA_900100365.1	86840	86840	type	True	86.1413	1451	1864	95	below_threshold
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	85.9149	1470	1864	95	below_threshold
Pseudomonas syringae pv. coryli	strain=NCPPB 4273	GCA_000972175.1	317659	317659	pathovar	True	85.8227	1438	1864	95	below_threshold
Pseudomonas syringae pv. coryli	strain=ICMP17001	GCA_001400235.1	317659	317659	pathovar	True	85.6777	1121	1864	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	85.3561	1489	1864	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	85.3159	1495	1864	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	79.4822	643	1864	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	79.3957	668	1864	95	below_threshold
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	77.1765	220	1864	95	below_threshold
Salinicola aestuarinus	strain=CPA62	GCA_003206645.1	1949082	1949082	type	True	75.9901	76	1864	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,115] [INFO] DFAST Taxonomy check result was written to GCF_001401155.1_PtrICMP9151_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,116] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference/checkm_data
[2024-01-24 13:58:36,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,175] [INFO] Task started: CheckM
[2024-01-24 13:58:36,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001401155.1_PtrICMP9151_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001401155.1_PtrICMP9151_genomic.fna/checkm_input GCF_001401155.1_PtrICMP9151_genomic.fna/checkm_result
[2024-01-24 13:59:29,434] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:29,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:29,459] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:29,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:29,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001401155.1_PtrICMP9151_genomic.fna/markers.fasta)
[2024-01-24 13:59:29,461] [INFO] Task started: Blastn
[2024-01-24 13:59:29,461] [INFO] Running command: blastn -query GCF_001401155.1_PtrICMP9151_genomic.fna/markers.fasta -db /var/lib/cwl/stg58bf8f57-7640-4859-bb08-64b810858ded/dqc_reference/reference_markers_gtdb.fasta -out GCF_001401155.1_PtrICMP9151_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:31,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:31,100] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:31,101] [INFO] Target genome list was writen to GCF_001401155.1_PtrICMP9151_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:31,112] [INFO] Task started: fastANI
[2024-01-24 13:59:31,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg72552eeb-c1aa-403e-a40d-c30692e7c23d/GCF_001401155.1_PtrICMP9151_genomic.fna.gz --refList GCF_001401155.1_PtrICMP9151_genomic.fna/target_genomes_gtdb.txt --output GCF_001401155.1_PtrICMP9151_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:45,206] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:45,219] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:45,219] [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_001401155.1	s__Pseudomonas_E tremae	100.0	1858	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.42	0.92	0.88	76	conclusive
GCF_002093745.1	s__Pseudomonas_E graminis_C	87.9793	1489	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000444135.1	s__Pseudomonas_E avellanae	86.7023	1331	1864	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_001466965.1	s__Pseudomonas_E syringae_Q	86.3723	1405	1864	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_001293775.1	s__Pseudomonas_E syringae_P	86.223	1419	1864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	86.1757	1427	1864	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	86.1393	1453	1864	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_002699855.1	s__Pseudomonas_E amygdali	85.8666	1373	1864	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_000507185.2	s__Pseudomonas_E syringae	85.7072	1485	1864	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	85.412	1442	1864	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 13:59:45,221] [INFO] GTDB search result was written to GCF_001401155.1_PtrICMP9151_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:45,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:45,225] [INFO] DFAST_QC result json was written to GCF_001401155.1_PtrICMP9151_genomic.fna/dqc_result.json
[2024-01-24 13:59:45,225] [INFO] DFAST_QC completed!
[2024-01-24 13:59:45,226] [INFO] Total running time: 0h2m0s