[2024-01-24 11:51:24,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference
[2024-01-24 11:51:26,158] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,159] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,159] [INFO] Running command: gunzip -c /var/lib/cwl/stgce287b2c-5b7e-4c09-87b2-b85e9a93003e/GCF_025562715.2_ASM2556271v2_genomic.fna.gz | prodigal -d GCF_025562715.2_ASM2556271v2_genomic.fna/cds.fna -a GCF_025562715.2_ASM2556271v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:42,082] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:42,082] [INFO] Task started: HMMsearch
[2024-01-24 11:51:42,082] [INFO] Running command: hmmsearch --tblout GCF_025562715.2_ASM2556271v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference/reference_markers.hmm GCF_025562715.2_ASM2556271v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:42,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:42,500] [INFO] Found 6/6 markers.
[2024-01-24 11:51:42,560] [INFO] Query marker FASTA was written to GCF_025562715.2_ASM2556271v2_genomic.fna/markers.fasta
[2024-01-24 11:51:42,560] [INFO] Task started: Blastn
[2024-01-24 11:51:42,561] [INFO] Running command: blastn -query GCF_025562715.2_ASM2556271v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference/reference_markers.fasta -out GCF_025562715.2_ASM2556271v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:43,309] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:43,371] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:43,371] [INFO] Target genome list was writen to GCF_025562715.2_ASM2556271v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:43,392] [INFO] Task started: fastANI
[2024-01-24 11:51:43,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgce287b2c-5b7e-4c09-87b2-b85e9a93003e/GCF_025562715.2_ASM2556271v2_genomic.fna.gz --refList GCF_025562715.2_ASM2556271v2_genomic.fna/target_genomes.txt --output GCF_025562715.2_ASM2556271v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:00,196] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:00,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:00,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:00,210] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:00,210] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:00,210] [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
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	81.6732	902	2112	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	81.5785	897	2112	95	below_threshold
Endozoicomonas numazuensis	strain=DSM 25634	GCA_000722635.1	1137799	1137799	type	True	78.4599	257	2112	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000710775.1	305900	305900	type	True	78.4545	169	2112	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	78.4426	275	2112	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	77.747	212	2112	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	77.6969	195	2112	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	77.6594	188	2112	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.3329	59	2112	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	76.3282	51	2112	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:00,212] [INFO] DFAST Taxonomy check result was written to GCF_025562715.2_ASM2556271v2_genomic.fna/tc_result.tsv
[2024-01-24 11:52:00,212] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:00,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:00,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference/checkm_data
[2024-01-24 11:52:00,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:00,282] [INFO] Task started: CheckM
[2024-01-24 11:52:00,282] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025562715.2_ASM2556271v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025562715.2_ASM2556271v2_genomic.fna/checkm_input GCF_025562715.2_ASM2556271v2_genomic.fna/checkm_result
[2024-01-24 11:52:51,996] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:51,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:52,024] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:52,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:52,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025562715.2_ASM2556271v2_genomic.fna/markers.fasta)
[2024-01-24 11:52:52,025] [INFO] Task started: Blastn
[2024-01-24 11:52:52,025] [INFO] Running command: blastn -query GCF_025562715.2_ASM2556271v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg27f91583-0681-45d9-b628-3a8c74cfeeee/dqc_reference/reference_markers_gtdb.fasta -out GCF_025562715.2_ASM2556271v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:53,060] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:53,065] [INFO] Selected 15 target genomes.
[2024-01-24 11:52:53,065] [INFO] Target genome list was writen to GCF_025562715.2_ASM2556271v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:53,073] [INFO] Task started: fastANI
[2024-01-24 11:52:53,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgce287b2c-5b7e-4c09-87b2-b85e9a93003e/GCF_025562715.2_ASM2556271v2_genomic.fna.gz --refList GCF_025562715.2_ASM2556271v2_genomic.fna/target_genomes_gtdb.txt --output GCF_025562715.2_ASM2556271v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:07,186] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:07,200] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:07,200] [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_001583435.1	s__Endozoicomonas montiporae	81.6028	910	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
GCF_000722635.1	s__Endozoicomonas numazuensis	78.5087	255	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562015.1	s__Endozoicomonas arenosclerae	78.4364	275	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710775.1	s__Endozoicomonas elysicola	78.432	170	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009653635.1	s__Endozoicomonas sp009653635	78.2827	218	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646945.1	s__Endozoicomonas ascidiicola	77.8124	211	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.76	98.76	0.78	0.78	2	-
GCA_004762125.1	s__Endozoicomonas sp004762125	77.7034	182	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002864045.1	s__Endozoicomonas acroporae	77.6966	193	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	-
GCA_017744115.1	s__Endozoicomonas sp017744115	77.4304	203	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCF_900108065.1	s__Marinobacterium lutimaris	76.3214	58	2112	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:07,202] [INFO] GTDB search result was written to GCF_025562715.2_ASM2556271v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:07,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:07,206] [INFO] DFAST_QC result json was written to GCF_025562715.2_ASM2556271v2_genomic.fna/dqc_result.json
[2024-01-24 11:53:07,206] [INFO] DFAST_QC completed!
[2024-01-24 11:53:07,206] [INFO] Total running time: 0h1m42s