[2024-01-24 11:30:49,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:30:49,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:30:49,469] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference
[2024-01-24 11:30:50,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:30:50,694] [INFO] Task started: Prodigal
[2024-01-24 11:30:50,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg55f1288a-7493-4e52-baf0-aed3e94d720f/GCF_012396255.1_ASM1239625v1_genomic.fna.gz | prodigal -d GCF_012396255.1_ASM1239625v1_genomic.fna/cds.fna -a GCF_012396255.1_ASM1239625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:31:06,445] [INFO] Task succeeded: Prodigal
[2024-01-24 11:31:06,445] [INFO] Task started: HMMsearch
[2024-01-24 11:31:06,445] [INFO] Running command: hmmsearch --tblout GCF_012396255.1_ASM1239625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference/reference_markers.hmm GCF_012396255.1_ASM1239625v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:31:06,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:31:06,727] [INFO] Found 6/6 markers.
[2024-01-24 11:31:06,771] [INFO] Query marker FASTA was written to GCF_012396255.1_ASM1239625v1_genomic.fna/markers.fasta
[2024-01-24 11:31:06,771] [INFO] Task started: Blastn
[2024-01-24 11:31:06,771] [INFO] Running command: blastn -query GCF_012396255.1_ASM1239625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference/reference_markers.fasta -out GCF_012396255.1_ASM1239625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:31:07,966] [INFO] Task succeeded: Blastn
[2024-01-24 11:31:07,971] [INFO] Selected 12 target genomes.
[2024-01-24 11:31:07,971] [INFO] Target genome list was writen to GCF_012396255.1_ASM1239625v1_genomic.fna/target_genomes.txt
[2024-01-24 11:31:08,014] [INFO] Task started: fastANI
[2024-01-24 11:31:08,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f1288a-7493-4e52-baf0-aed3e94d720f/GCF_012396255.1_ASM1239625v1_genomic.fna.gz --refList GCF_012396255.1_ASM1239625v1_genomic.fna/target_genomes.txt --output GCF_012396255.1_ASM1239625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:31:21,442] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:21,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:31:21,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:31:21,456] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:31:21,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:31:21,456] [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 sputi	strain=ATCC 29627	GCA_012396255.1	36823	36823	type	True	100.0	1623	1625	95	conclusive
Gordonia sputi	strain=NBRC 100414	GCA_000248055.2	36823	36823	type	True	99.9732	1563	1625	95	conclusive
Gordonia aichiensis	strain=NBRC 108223	GCA_000332975.1	36820	36820	type	True	84.672	1244	1625	95	below_threshold
Gordonia otitidis	strain=NBRC 100426	GCA_000248075.2	249058	249058	type	True	83.9314	1157	1625	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	79.5202	687	1625	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	79.4972	671	1625	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	79.4862	676	1625	95	below_threshold
Gordonia polyisoprenivorans	strain=ATCC BAA-14	GCA_012396285.1	84595	84595	type	True	79.4571	810	1625	95	below_threshold
Gordonia lacunae	strain=BS2	GCA_002149015.1	417102	417102	type	True	79.2117	677	1625	95	below_threshold
Gordonia rhizosphera	strain=NBRC 16068	GCA_000298195.1	83341	83341	type	True	79.0903	642	1625	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	79.0569	723	1625	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	78.994	673	1625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:31:21,458] [INFO] DFAST Taxonomy check result was written to GCF_012396255.1_ASM1239625v1_genomic.fna/tc_result.tsv
[2024-01-24 11:31:21,458] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:31:21,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:31:21,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference/checkm_data
[2024-01-24 11:31:21,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:31:21,505] [INFO] Task started: CheckM
[2024-01-24 11:31:21,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396255.1_ASM1239625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396255.1_ASM1239625v1_genomic.fna/checkm_input GCF_012396255.1_ASM1239625v1_genomic.fna/checkm_result
[2024-01-24 11:32:10,650] [INFO] Task succeeded: CheckM
[2024-01-24 11:32:10,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:32:10,674] [INFO] ===== Completeness check finished =====
[2024-01-24 11:32:10,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:32:10,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396255.1_ASM1239625v1_genomic.fna/markers.fasta)
[2024-01-24 11:32:10,675] [INFO] Task started: Blastn
[2024-01-24 11:32:10,675] [INFO] Running command: blastn -query GCF_012396255.1_ASM1239625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfaef0c5-b17b-4e38-9bad-cb70a0e07e53/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396255.1_ASM1239625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:32:12,488] [INFO] Task succeeded: Blastn
[2024-01-24 11:32:12,493] [INFO] Selected 11 target genomes.
[2024-01-24 11:32:12,493] [INFO] Target genome list was writen to GCF_012396255.1_ASM1239625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:32:13,053] [INFO] Task started: fastANI
[2024-01-24 11:32:13,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg55f1288a-7493-4e52-baf0-aed3e94d720f/GCF_012396255.1_ASM1239625v1_genomic.fna.gz --refList GCF_012396255.1_ASM1239625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396255.1_ASM1239625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:32:25,386] [INFO] Task succeeded: fastANI
[2024-01-24 11:32:25,399] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:32:25,400] [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_000248055.1	s__Gordonia sputi	99.9732	1563	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.92	96.52	0.90	0.84	5	conclusive
GCF_001186365.1	s__Gordonia jacobaea	92.6405	1439	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.30	95.68	0.92	0.90	5	-
GCF_000332975.1	s__Gordonia aichiensis	84.672	1244	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000248075.1	s__Gordonia otitidis	83.9295	1157	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241325.1	s__Gordonia polyisoprenivorans	79.5152	796	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.60	97.62	0.90	0.79	11	-
GCF_000298235.1	s__Gordonia namibiensis	79.4867	676	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000327325.1	s__Gordonia rubripertincta	79.4867	672	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_000298195.1	s__Gordonia rhizosphera	79.0909	642	1625	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	79.0507	723	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700145.1	s__Gordonia sp002700145	79.019	642	1625	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	79.0071	671	1625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.33	98.32	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:32:25,401] [INFO] GTDB search result was written to GCF_012396255.1_ASM1239625v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:32:25,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:32:25,406] [INFO] DFAST_QC result json was written to GCF_012396255.1_ASM1239625v1_genomic.fna/dqc_result.json
[2024-01-24 11:32:25,406] [INFO] DFAST_QC completed!
[2024-01-24 11:32:25,406] [INFO] Total running time: 0h1m36s