[2024-01-24 13:32:17,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:17,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:17,710] [INFO] DQC Reference Directory: /var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference
[2024-01-24 13:32:19,101] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,102] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg22dff359-a89f-4623-ba47-277c7e777ad9/GCF_012396615.1_ASM1239661v1_genomic.fna.gz | prodigal -d GCF_012396615.1_ASM1239661v1_genomic.fna/cds.fna -a GCF_012396615.1_ASM1239661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:26,098] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:26,099] [INFO] Task started: HMMsearch
[2024-01-24 13:32:26,099] [INFO] Running command: hmmsearch --tblout GCF_012396615.1_ASM1239661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference/reference_markers.hmm GCF_012396615.1_ASM1239661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:26,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:26,399] [INFO] Found 6/6 markers.
[2024-01-24 13:32:26,431] [INFO] Query marker FASTA was written to GCF_012396615.1_ASM1239661v1_genomic.fna/markers.fasta
[2024-01-24 13:32:26,431] [INFO] Task started: Blastn
[2024-01-24 13:32:26,432] [INFO] Running command: blastn -query GCF_012396615.1_ASM1239661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference/reference_markers.fasta -out GCF_012396615.1_ASM1239661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:27,205] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:27,208] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:27,208] [INFO] Target genome list was writen to GCF_012396615.1_ASM1239661v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:27,218] [INFO] Task started: fastANI
[2024-01-24 13:32:27,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg22dff359-a89f-4623-ba47-277c7e777ad9/GCF_012396615.1_ASM1239661v1_genomic.fna.gz --refList GCF_012396615.1_ASM1239661v1_genomic.fna/target_genomes.txt --output GCF_012396615.1_ASM1239661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:39,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:39,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:39,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:39,172] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:39,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:39,173] [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
Rothia terrae	strain=LMG 23708	GCA_012396615.1	396015	396015	type	True	100.0	804	804	95	conclusive
Rothia aerolata	strain=CCM 8669	GCA_014635585.1	1812262	1812262	type	True	79.1007	203	804	95	below_threshold
Rothia mucilaginosa	strain=ATCC 25296	GCA_000175615.1	43675	43675	suspected-type	True	78.3867	132	804	95	below_threshold
Rothia dentocariosa	strain=ATCC 17931	GCA_000164695.2	2047	2047	type	True	77.9691	88	804	95	below_threshold
Rothia dentocariosa	strain=NCTC10917	GCA_900455895.1	2047	2047	type	True	77.9682	88	804	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	77.3693	52	804	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	77.0641	52	804	95	below_threshold
Arthrobacter psychrolactophilus	strain=B7	GCA_003219795.1	92442	92442	type	True	76.7065	53	804	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	76.6115	54	804	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_900177335.1	1049583	1049583	type	True	76.4305	52	804	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	76.4305	52	804	95	below_threshold
Arthrobacter glacialis	strain=HLT2-12-2	GCA_002909445.1	1664	1664	type	True	76.3036	51	804	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	76.0986	51	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:39,174] [INFO] DFAST Taxonomy check result was written to GCF_012396615.1_ASM1239661v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:39,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:39,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:39,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference/checkm_data
[2024-01-24 13:32:39,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:39,206] [INFO] Task started: CheckM
[2024-01-24 13:32:39,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396615.1_ASM1239661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396615.1_ASM1239661v1_genomic.fna/checkm_input GCF_012396615.1_ASM1239661v1_genomic.fna/checkm_result
[2024-01-24 13:33:06,744] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:06,745] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,760] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:06,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:06,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396615.1_ASM1239661v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:06,761] [INFO] Task started: Blastn
[2024-01-24 13:33:06,761] [INFO] Running command: blastn -query GCF_012396615.1_ASM1239661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9ee021d-9cc5-4fa1-b238-6850c9154ec3/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396615.1_ASM1239661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:07,956] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:07,959] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:07,959] [INFO] Target genome list was writen to GCF_012396615.1_ASM1239661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:07,980] [INFO] Task started: fastANI
[2024-01-24 13:33:07,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg22dff359-a89f-4623-ba47-277c7e777ad9/GCF_012396615.1_ASM1239661v1_genomic.fna.gz --refList GCF_012396615.1_ASM1239661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396615.1_ASM1239661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:16,043] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:16,055] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:16,055] [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_012396615.1	s__Rothia terrae	100.0	804	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.55	98.48	0.95	0.93	4	conclusive
GCF_016924835.1	s__Rothia sp016924835	79.6384	273	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	99.38	99.38	0.96	0.96	2	-
GCF_014635585.1	s__Rothia aerolata	79.1007	203	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901875305.1	s__Rothia sp902373285	78.4341	126	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.53	97.34	0.97	0.96	6	-
GCA_019115985.1	s__Rothia avicola	78.4121	176	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418375.1	s__Rothia sp002418375	78.3115	177	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.17	96.17	0.93	0.93	2	-
GCF_004569295.1	s__Rothia nasimurium_B	78.2828	181	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014217215.1	s__Rothia nasimurium_C	78.2463	197	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	98.36	98.36	0.95	0.95	2	-
GCA_015265375.1	s__Rothia sp015265375	78.1634	127	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.30	95.30	0.97	0.97	2	-
GCF_001548235.1	s__Rothia mucilaginosa_B	78.1548	136	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	95.72	95.51	0.97	0.96	3	-
GCF_002087015.1	s__Rothia nasimurium_A	78.1019	162	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808955.1	s__Rothia sp001808955	77.9252	141	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	96.04	95.53	0.94	0.90	20	-
GCF_001061665.1	s__Rothia mucilaginosa_A	77.895	119	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Rothia	95.0	97.28	96.59	0.94	0.92	10	-
GCF_001580365.1	s__Kocuria turfanensis	76.6115	54	804	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,056] [INFO] GTDB search result was written to GCF_012396615.1_ASM1239661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:16,057] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:16,060] [INFO] DFAST_QC result json was written to GCF_012396615.1_ASM1239661v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:16,061] [INFO] DFAST_QC completed!
[2024-01-24 13:33:16,061] [INFO] Total running time: 0h0m58s