[2024-01-24 13:33:11,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:11,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:11,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference
[2024-01-24 13:33:12,625] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,626] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,626] [INFO] Running command: gunzip -c /var/lib/cwl/stgf90ae407-ee9b-4153-8558-b41746edfcf3/GCF_007745435.1_ASM774543v1_genomic.fna.gz | prodigal -d GCF_007745435.1_ASM774543v1_genomic.fna/cds.fna -a GCF_007745435.1_ASM774543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:29,534] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:29,535] [INFO] Task started: HMMsearch
[2024-01-24 13:33:29,535] [INFO] Running command: hmmsearch --tblout GCF_007745435.1_ASM774543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference/reference_markers.hmm GCF_007745435.1_ASM774543v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:29,866] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:29,868] [INFO] Found 6/6 markers.
[2024-01-24 13:33:29,915] [INFO] Query marker FASTA was written to GCF_007745435.1_ASM774543v1_genomic.fna/markers.fasta
[2024-01-24 13:33:29,916] [INFO] Task started: Blastn
[2024-01-24 13:33:29,916] [INFO] Running command: blastn -query GCF_007745435.1_ASM774543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference/reference_markers.fasta -out GCF_007745435.1_ASM774543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:30,533] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:30,537] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:30,537] [INFO] Target genome list was writen to GCF_007745435.1_ASM774543v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:30,556] [INFO] Task started: fastANI
[2024-01-24 13:33:30,556] [INFO] Running command: fastANI --query /var/lib/cwl/stgf90ae407-ee9b-4153-8558-b41746edfcf3/GCF_007745435.1_ASM774543v1_genomic.fna.gz --refList GCF_007745435.1_ASM774543v1_genomic.fna/target_genomes.txt --output GCF_007745435.1_ASM774543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:50,807] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:50,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:50,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:50,820] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:50,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:50,821] [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
Calycomorphotria hydatis	strain=V22	GCA_007745435.1	2528027	2528027	type	True	100.0	1719	1721	95	conclusive
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.2229	90	1721	95	below_threshold
Rubinisphaera italica	strain=Pan54	GCA_007859715.1	2527969	2527969	type	True	76.1873	53	1721	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	76.0651	67	1721	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	76.0374	59	1721	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	75.7699	75	1721	95	below_threshold
Schlesneria paludicola	strain=DSM 18645	GCA_000255655.1	360056	360056	type	True	75.6865	50	1721	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.5168	76	1721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:50,823] [INFO] DFAST Taxonomy check result was written to GCF_007745435.1_ASM774543v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:50,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:50,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:50,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference/checkm_data
[2024-01-24 13:33:50,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:50,875] [INFO] Task started: CheckM
[2024-01-24 13:33:50,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007745435.1_ASM774543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007745435.1_ASM774543v1_genomic.fna/checkm_input GCF_007745435.1_ASM774543v1_genomic.fna/checkm_result
[2024-01-24 13:34:38,987] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:38,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:39,011] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:39,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:39,012] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007745435.1_ASM774543v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:39,013] [INFO] Task started: Blastn
[2024-01-24 13:34:39,013] [INFO] Running command: blastn -query GCF_007745435.1_ASM774543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45ee253a-57e2-4e3d-b196-4a33bf22e8be/dqc_reference/reference_markers_gtdb.fasta -out GCF_007745435.1_ASM774543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:39,787] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:39,791] [INFO] Selected 23 target genomes.
[2024-01-24 13:34:39,791] [INFO] Target genome list was writen to GCF_007745435.1_ASM774543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:39,830] [INFO] Task started: fastANI
[2024-01-24 13:34:39,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgf90ae407-ee9b-4153-8558-b41746edfcf3/GCF_007745435.1_ASM774543v1_genomic.fna.gz --refList GCF_007745435.1_ASM774543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007745435.1_ASM774543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:02,660] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:02,676] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:02,677] [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_007745435.1	s__Calycomorphotria hydatis	100.0	1719	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007744515.1	s__Calycomorphotria sp007744515	76.3505	144	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	76.1132	89	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.919	65	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007748155.1	s__Gimesia panareensis	75.8111	63	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.7745	97	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699955.1	s__JABISG01 sp018699955	75.6577	52	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.6252	65	1721	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:02,679] [INFO] GTDB search result was written to GCF_007745435.1_ASM774543v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:02,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:02,683] [INFO] DFAST_QC result json was written to GCF_007745435.1_ASM774543v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:02,683] [INFO] DFAST_QC completed!
[2024-01-24 13:35:02,683] [INFO] Total running time: 0h1m51s