[2024-01-24 12:06:24,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,813] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference
[2024-01-24 12:06:26,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,175] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a36c2d6-f404-43d1-999c-46d6577702f5/GCF_002864045.1_ASM286404v1_genomic.fna.gz | prodigal -d GCF_002864045.1_ASM286404v1_genomic.fna/cds.fna -a GCF_002864045.1_ASM286404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:41,542] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:41,543] [INFO] Task started: HMMsearch
[2024-01-24 12:06:41,543] [INFO] Running command: hmmsearch --tblout GCF_002864045.1_ASM286404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference/reference_markers.hmm GCF_002864045.1_ASM286404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:41,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:41,850] [INFO] Found 6/6 markers.
[2024-01-24 12:06:41,907] [INFO] Query marker FASTA was written to GCF_002864045.1_ASM286404v1_genomic.fna/markers.fasta
[2024-01-24 12:06:41,908] [INFO] Task started: Blastn
[2024-01-24 12:06:41,908] [INFO] Running command: blastn -query GCF_002864045.1_ASM286404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference/reference_markers.fasta -out GCF_002864045.1_ASM286404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:42,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:42,694] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:42,694] [INFO] Target genome list was writen to GCF_002864045.1_ASM286404v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:42,699] [INFO] Task started: fastANI
[2024-01-24 12:06:42,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a36c2d6-f404-43d1-999c-46d6577702f5/GCF_002864045.1_ASM286404v1_genomic.fna.gz --refList GCF_002864045.1_ASM286404v1_genomic.fna/target_genomes.txt --output GCF_002864045.1_ASM286404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:03,815] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:03,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:03,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:03,823] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:03,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:03,823] [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 acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	100.0	1860	1867	95	conclusive
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	84.9076	946	1867	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000710775.1	305900	305900	type	True	81.2446	788	1867	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000373945.1	305900	305900	type	True	81.2035	779	1867	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	78.6853	396	1867	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	77.3408	193	1867	95	below_threshold
Endozoicomonas arenosclerae	strain=ab112	GCA_001562015.1	1633495	1633495	type	True	77.2215	182	1867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:03,825] [INFO] DFAST Taxonomy check result was written to GCF_002864045.1_ASM286404v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:03,825] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:03,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:03,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference/checkm_data
[2024-01-24 12:07:03,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:03,883] [INFO] Task started: CheckM
[2024-01-24 12:07:03,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002864045.1_ASM286404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002864045.1_ASM286404v1_genomic.fna/checkm_input GCF_002864045.1_ASM286404v1_genomic.fna/checkm_result
[2024-01-24 12:07:50,458] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:50,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,479] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:50,479] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:50,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002864045.1_ASM286404v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:50,479] [INFO] Task started: Blastn
[2024-01-24 12:07:50,480] [INFO] Running command: blastn -query GCF_002864045.1_ASM286404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf55d53-f029-4b3b-b24d-932a5f433340/dqc_reference/reference_markers_gtdb.fasta -out GCF_002864045.1_ASM286404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:51,610] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:51,614] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:51,614] [INFO] Target genome list was writen to GCF_002864045.1_ASM286404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:51,619] [INFO] Task started: fastANI
[2024-01-24 12:07:51,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a36c2d6-f404-43d1-999c-46d6577702f5/GCF_002864045.1_ASM286404v1_genomic.fna.gz --refList GCF_002864045.1_ASM286404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002864045.1_ASM286404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:08,993] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:08,999] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:09,000] [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_002864045.1	s__Endozoicomonas acroporae	100.0	1860	1867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	conclusive
GCA_017744115.1	s__Endozoicomonas sp017744115	94.1387	1511	1867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCF_001647025.1	s__Endozoicomonas atrinae	84.8888	948	1867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299555.1	s__Endozoicomonas sp900299555	81.4199	778	1867	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	81.2094	790	1867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:09,001] [INFO] GTDB search result was written to GCF_002864045.1_ASM286404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:09,002] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:09,005] [INFO] DFAST_QC result json was written to GCF_002864045.1_ASM286404v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:09,005] [INFO] DFAST_QC completed!
[2024-01-24 12:08:09,005] [INFO] Total running time: 0h1m44s