[2024-01-24 13:37:19,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:19,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:19,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference
[2024-01-24 13:37:21,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:21,274] [INFO] Task started: Prodigal
[2024-01-24 13:37:21,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg4dac3f80-26ac-4766-b9d1-2e5f3cc868a5/GCF_021556435.1_ASM2155643v1_genomic.fna.gz | prodigal -d GCF_021556435.1_ASM2155643v1_genomic.fna/cds.fna -a GCF_021556435.1_ASM2155643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:39,844] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:39,844] [INFO] Task started: HMMsearch
[2024-01-24 13:37:39,844] [INFO] Running command: hmmsearch --tblout GCF_021556435.1_ASM2155643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference/reference_markers.hmm GCF_021556435.1_ASM2155643v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:40,194] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:40,196] [INFO] Found 6/6 markers.
[2024-01-24 13:37:40,255] [INFO] Query marker FASTA was written to GCF_021556435.1_ASM2155643v1_genomic.fna/markers.fasta
[2024-01-24 13:37:40,255] [INFO] Task started: Blastn
[2024-01-24 13:37:40,255] [INFO] Running command: blastn -query GCF_021556435.1_ASM2155643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference/reference_markers.fasta -out GCF_021556435.1_ASM2155643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:41,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:41,407] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:41,407] [INFO] Target genome list was writen to GCF_021556435.1_ASM2155643v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:41,419] [INFO] Task started: fastANI
[2024-01-24 13:37:41,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dac3f80-26ac-4766-b9d1-2e5f3cc868a5/GCF_021556435.1_ASM2155643v1_genomic.fna.gz --refList GCF_021556435.1_ASM2155643v1_genomic.fna/target_genomes.txt --output GCF_021556435.1_ASM2155643v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:56,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:56,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:56,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:56,987] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:56,987] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:56,987] [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
Gordonia mangrovi	strain=HNM0687	GCA_009828195.1	2665643	2665643	type	True	86.5125	1308	1728	95	below_threshold
Gordonia mangrovi	strain=HNM0687	GCA_024734075.1	2665643	2665643	type	True	86.4631	1310	1728	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	81.3642	1040	1728	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	80.5612	943	1728	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	80.4363	935	1728	95	below_threshold
Gordonia bronchialis	strain=FDAARGOS_1594	GCA_020731255.1	2054	2054	type	True	80.2448	803	1728	95	below_threshold
Gordonia bronchialis	strain=NCTC10667	GCA_900450805.1	2054	2054	type	True	80.2251	833	1728	95	below_threshold
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	79.9586	778	1728	95	below_threshold
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	79.9202	768	1728	95	below_threshold
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	79.9199	790	1728	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	79.9164	751	1728	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.7612	766	1728	95	below_threshold
Gordonia sputi	strain=ATCC 29627	GCA_012396255.1	36823	36823	type	True	79.1707	645	1728	95	below_threshold
Gordonia sihwensis	strain=NBRC 108236	GCA_000333035.1	173559	173559	type	True	78.6953	468	1728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:56,989] [INFO] DFAST Taxonomy check result was written to GCF_021556435.1_ASM2155643v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:56,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:56,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:56,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference/checkm_data
[2024-01-24 13:37:56,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:57,043] [INFO] Task started: CheckM
[2024-01-24 13:37:57,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021556435.1_ASM2155643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021556435.1_ASM2155643v1_genomic.fna/checkm_input GCF_021556435.1_ASM2155643v1_genomic.fna/checkm_result
[2024-01-24 13:38:59,970] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:59,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:59,993] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:59,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:59,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021556435.1_ASM2155643v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:59,994] [INFO] Task started: Blastn
[2024-01-24 13:38:59,994] [INFO] Running command: blastn -query GCF_021556435.1_ASM2155643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1cd7f62-fea6-41fa-a161-aa5f666f0cfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_021556435.1_ASM2155643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:01,574] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:01,577] [INFO] Selected 14 target genomes.
[2024-01-24 13:39:01,577] [INFO] Target genome list was writen to GCF_021556435.1_ASM2155643v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:01,602] [INFO] Task started: fastANI
[2024-01-24 13:39:01,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg4dac3f80-26ac-4766-b9d1-2e5f3cc868a5/GCF_021556435.1_ASM2155643v1_genomic.fna.gz --refList GCF_021556435.1_ASM2155643v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021556435.1_ASM2155643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:18,045] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:18,062] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:18,062] [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
GCA_002700145.1	s__Gordonia sp002700145	98.3698	1477	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009828195.1	s__Gordonia sp009828195	86.5044	1309	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855095.1	s__Gordonia insulae	81.3705	1039	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797825.1	s__Gordonia sp003797825	81.143	1073	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004193205.1	s__Gordonia sediminis	80.5708	988	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298195.1	s__Gordonia rhizosphera	80.5634	943	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014673215.1	s__Gordonia hankookensis	80.4324	936	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
GCF_009862785.1	s__Gordonia sp009862785	80.3753	912	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024785.1	s__Gordonia bronchialis	80.2525	805	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001485495.1	s__Gordonia desulfuricans	80.039	765	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	98.77	0.95	0.92	3	-
GCF_002149015.1	s__Gordonia lacunae	79.8814	785	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298235.1	s__Gordonia namibiensis	79.7544	767	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	79.538	772	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333035.1	s__Gordonia sihwensis	78.7002	467	1728	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:18,064] [INFO] GTDB search result was written to GCF_021556435.1_ASM2155643v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:18,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:18,068] [INFO] DFAST_QC result json was written to GCF_021556435.1_ASM2155643v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:18,069] [INFO] DFAST_QC completed!
[2024-01-24 13:39:18,069] [INFO] Total running time: 0h1m58s