[2024-01-24 11:51:23,362] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference
[2024-01-24 11:51:24,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:24,666] [INFO] Task started: Prodigal
[2024-01-24 11:51:24,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ff7f86f-859a-4b9e-9136-d3a7d163cf96/GCF_014230085.1_ASM1423008v1_genomic.fna.gz | prodigal -d GCF_014230085.1_ASM1423008v1_genomic.fna/cds.fna -a GCF_014230085.1_ASM1423008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:50,344] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:50,345] [INFO] Task started: HMMsearch
[2024-01-24 11:51:50,345] [INFO] Running command: hmmsearch --tblout GCF_014230085.1_ASM1423008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference/reference_markers.hmm GCF_014230085.1_ASM1423008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:50,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:50,611] [INFO] Found 6/6 markers.
[2024-01-24 11:51:50,654] [INFO] Query marker FASTA was written to GCF_014230085.1_ASM1423008v1_genomic.fna/markers.fasta
[2024-01-24 11:51:50,655] [INFO] Task started: Blastn
[2024-01-24 11:51:50,655] [INFO] Running command: blastn -query GCF_014230085.1_ASM1423008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference/reference_markers.fasta -out GCF_014230085.1_ASM1423008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:51,262] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:51,268] [INFO] Selected 24 target genomes.
[2024-01-24 11:51:51,269] [INFO] Target genome list was writen to GCF_014230085.1_ASM1423008v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:51,288] [INFO] Task started: fastANI
[2024-01-24 11:51:51,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ff7f86f-859a-4b9e-9136-d3a7d163cf96/GCF_014230085.1_ASM1423008v1_genomic.fna.gz --refList GCF_014230085.1_ASM1423008v1_genomic.fna/target_genomes.txt --output GCF_014230085.1_ASM1423008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:07,685] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:07,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:07,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:07,694] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:07,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:07,695] [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
Ruficoccus amylovorans	strain=JCM31066	GCA_014230085.1	1804625	1804625	type	True	100.0	1470	1472	95	conclusive
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.8755	59	1472	95	below_threshold
Cerasicoccus arenae	strain=KCTC 12870	GCA_016595555.1	424488	424488	type	True	76.4756	79	1472	95	below_threshold
Cerasicoccus arenae	strain=KCTC 12870	GCA_014651635.1	424488	424488	type	True	76.4475	80	1472	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.3638	70	1472	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.3164	101	1472	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.2064	64	1472	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.1656	81	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:07,697] [INFO] DFAST Taxonomy check result was written to GCF_014230085.1_ASM1423008v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:07,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:07,699] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:07,699] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference/checkm_data
[2024-01-24 11:52:07,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:07,748] [INFO] Task started: CheckM
[2024-01-24 11:52:07,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014230085.1_ASM1423008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014230085.1_ASM1423008v1_genomic.fna/checkm_input GCF_014230085.1_ASM1423008v1_genomic.fna/checkm_result
[2024-01-24 11:53:15,618] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:15,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:15,642] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:15,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:15,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014230085.1_ASM1423008v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:15,643] [INFO] Task started: Blastn
[2024-01-24 11:53:15,644] [INFO] Running command: blastn -query GCF_014230085.1_ASM1423008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f3f480b-c1b3-4612-b425-2131b44f8c2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014230085.1_ASM1423008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:16,527] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:16,532] [INFO] Selected 28 target genomes.
[2024-01-24 11:53:16,532] [INFO] Target genome list was writen to GCF_014230085.1_ASM1423008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:16,588] [INFO] Task started: fastANI
[2024-01-24 11:53:16,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ff7f86f-859a-4b9e-9136-d3a7d163cf96/GCF_014230085.1_ASM1423008v1_genomic.fna.gz --refList GCF_014230085.1_ASM1423008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014230085.1_ASM1423008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:32,031] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:32,046] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:32,047] [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_014230085.1	s__Ruficoccus amylovorans	100.0	1470	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__KCTC-12870;g__Ruficoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009772895.1	s__WOUP01 sp009772895	77.334	102	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Verruco-01;g__WOUP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569245.1	s__UBA953 sp003569245	77.2115	74	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871725.1	s__UBA953 sp016871725	76.8021	80	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA953	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070825.1	s__MWDT01 sp002070825	76.7373	58	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	97.04	96.87	0.67	0.67	3	-
GCA_019136515.1	s__CAJCBL01 sp019136515	76.676	111	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAJCBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190985.1	s__Lacunisphaera sp016190985	76.6333	89	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746835.1	s__Lacunisphaera limnophila	76.6325	101	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898675.1	s__Lacunisphaera sp903898675	76.5752	89	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
GCA_903868455.1	s__UBA8828 sp903868455	76.4161	83	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__UBA953;g__UBA8828	95.0	99.27	99.12	0.85	0.83	7	-
GCA_016795545.1	s__Lacunisphaera sp016795545	76.2317	70	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001604565.1	s__Verruco-01 sp001604565	76.1934	65	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Verruco-01;g__Verruco-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134215.1	s__SLLG01 sp007134215	76.1607	93	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Verruco-01;g__SLLG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928295.1	s__Verruco-01 sp016928295	76.0579	50	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Verruco-01;g__Verruco-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876795.1	s__Rariglobus sp903876795	75.9438	90	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007695295.1	s__REEB01 sp007695295	75.7797	90	1472	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__REEB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:32,048] [INFO] GTDB search result was written to GCF_014230085.1_ASM1423008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:32,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:32,052] [INFO] DFAST_QC result json was written to GCF_014230085.1_ASM1423008v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:32,052] [INFO] DFAST_QC completed!
[2024-01-24 11:53:32,052] [INFO] Total running time: 0h2m9s