[2024-01-25 18:14:50,786] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:50,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:50,787] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference
[2024-01-25 18:14:51,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:51,868] [INFO] Task started: Prodigal
[2024-01-25 18:14:51,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg40acd388-e5b8-4c28-9da0-d13a640da983/GCF_017377795.1_ASM1737779v1_genomic.fna.gz | prodigal -d GCF_017377795.1_ASM1737779v1_genomic.fna/cds.fna -a GCF_017377795.1_ASM1737779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:14,772] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:14,773] [INFO] Task started: HMMsearch
[2024-01-25 18:15:14,773] [INFO] Running command: hmmsearch --tblout GCF_017377795.1_ASM1737779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference/reference_markers.hmm GCF_017377795.1_ASM1737779v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:15,012] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:15,013] [INFO] Found 6/6 markers.
[2024-01-25 18:15:15,059] [INFO] Query marker FASTA was written to GCF_017377795.1_ASM1737779v1_genomic.fna/markers.fasta
[2024-01-25 18:15:15,059] [INFO] Task started: Blastn
[2024-01-25 18:15:15,059] [INFO] Running command: blastn -query GCF_017377795.1_ASM1737779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference/reference_markers.fasta -out GCF_017377795.1_ASM1737779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:16,086] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:16,088] [INFO] Selected 12 target genomes.
[2024-01-25 18:15:16,089] [INFO] Target genome list was writen to GCF_017377795.1_ASM1737779v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:16,094] [INFO] Task started: fastANI
[2024-01-25 18:15:16,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg40acd388-e5b8-4c28-9da0-d13a640da983/GCF_017377795.1_ASM1737779v1_genomic.fna.gz --refList GCF_017377795.1_ASM1737779v1_genomic.fna/target_genomes.txt --output GCF_017377795.1_ASM1737779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:29,240] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:29,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:29,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:29,249] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:29,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:29,249] [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
Williamsia soli	strain=C17	GCA_017377795.1	364929	364929	type	True	100.0	2009	2011	95	conclusive
Williamsia limnetica	strain=DSM 45521	GCA_003217475.1	882452	882452	type	True	86.4172	1517	2011	95	below_threshold
Williamsia muralis	strain=NBRC 105860	GCA_001598915.1	85044	85044	suspected-type	True	80.1636	933	2011	95	below_threshold
Williamsia muralis	strain=DSM 44343	GCA_003634525.1	85044	85044	suspected-type	True	80.1411	936	2011	95	below_threshold
Williamsia maris	strain=DSM 44693	GCA_024171815.1	72806	72806	type	True	78.5324	568	2011	95	below_threshold
Gordonia amicalis	strain=DSM 44461	GCA_012395955.1	89053	89053	type	True	78.2813	493	2011	95	below_threshold
Gordonia polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	77.9883	461	2011	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	77.9788	546	2011	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	77.4717	361	2011	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	77.4631	362	2011	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	77.4189	363	2011	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	77.3058	325	2011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:29,251] [INFO] DFAST Taxonomy check result was written to GCF_017377795.1_ASM1737779v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:29,252] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:29,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:29,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference/checkm_data
[2024-01-25 18:15:29,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:29,310] [INFO] Task started: CheckM
[2024-01-25 18:15:29,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017377795.1_ASM1737779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017377795.1_ASM1737779v1_genomic.fna/checkm_input GCF_017377795.1_ASM1737779v1_genomic.fna/checkm_result
[2024-01-25 18:16:41,788] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:41,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:41,812] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:41,812] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:41,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017377795.1_ASM1737779v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:41,813] [INFO] Task started: Blastn
[2024-01-25 18:16:41,813] [INFO] Running command: blastn -query GCF_017377795.1_ASM1737779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeadc826-8513-4b06-8357-f69c8f273e9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017377795.1_ASM1737779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:43,425] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:43,428] [INFO] Selected 9 target genomes.
[2024-01-25 18:16:43,428] [INFO] Target genome list was writen to GCF_017377795.1_ASM1737779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:43,440] [INFO] Task started: fastANI
[2024-01-25 18:16:43,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg40acd388-e5b8-4c28-9da0-d13a640da983/GCF_017377795.1_ASM1737779v1_genomic.fna.gz --refList GCF_017377795.1_ASM1737779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017377795.1_ASM1737779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:56,160] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:56,167] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:56,168] [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_017377795.1	s__Williamsia sp017377795	100.0	2009	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002095395.1	s__Williamsia sp002095395	92.9585	1539	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002095435.2	s__Williamsia sp002095435	90.6311	1585	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.0	98.25	98.25	0.87	0.87	2	-
GCF_003217475.1	s__Williamsia limnetica	86.4304	1514	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598915.1	s__Williamsia muralis	80.1757	931	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.715	98.29	96.70	0.92	0.87	4	-
GCF_000717275.1	s__Williamsia arboriphila	80.1467	918	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.715	100.00	100.00	1.00	1.00	2	-
GCF_002735905.1	s__Williamsia muralis_A	80.1322	917	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.5136	98.65	98.65	0.84	0.84	2	-
GCA_003202005.1	s__Williamsia faeni	80.0704	854	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Williamsia	95.0	97.44	97.44	0.90	0.90	2	-
GCF_011801125.1	s__Nocardia brasiliensis_C	77.2293	375	2011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:56,170] [INFO] GTDB search result was written to GCF_017377795.1_ASM1737779v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:56,170] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:56,173] [INFO] DFAST_QC result json was written to GCF_017377795.1_ASM1737779v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:56,173] [INFO] DFAST_QC completed!
[2024-01-25 18:16:56,173] [INFO] Total running time: 0h2m5s