[2024-01-24 13:01:49,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:49,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:49,670] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference
[2024-01-24 13:01:51,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,039] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgb19bbd89-3479-4e55-9483-4e52bea7cb13/GCF_000716975.1_ASM71697v1_genomic.fna.gz | prodigal -d GCF_000716975.1_ASM71697v1_genomic.fna/cds.fna -a GCF_000716975.1_ASM71697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:11,649] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:11,650] [INFO] Task started: HMMsearch
[2024-01-24 13:02:11,650] [INFO] Running command: hmmsearch --tblout GCF_000716975.1_ASM71697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference/reference_markers.hmm GCF_000716975.1_ASM71697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:12,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:12,039] [INFO] Found 6/6 markers.
[2024-01-24 13:02:12,092] [INFO] Query marker FASTA was written to GCF_000716975.1_ASM71697v1_genomic.fna/markers.fasta
[2024-01-24 13:02:12,092] [INFO] Task started: Blastn
[2024-01-24 13:02:12,092] [INFO] Running command: blastn -query GCF_000716975.1_ASM71697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference/reference_markers.fasta -out GCF_000716975.1_ASM71697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:13,363] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:13,368] [INFO] Selected 5 target genomes.
[2024-01-24 13:02:13,368] [INFO] Target genome list was writen to GCF_000716975.1_ASM71697v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:13,371] [INFO] Task started: fastANI
[2024-01-24 13:02:13,371] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19bbd89-3479-4e55-9483-4e52bea7cb13/GCF_000716975.1_ASM71697v1_genomic.fna.gz --refList GCF_000716975.1_ASM71697v1_genomic.fna/target_genomes.txt --output GCF_000716975.1_ASM71697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:22,909] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:22,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:22,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:22,922] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:02:22,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:22,923] [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 terrae	strain=NRRL B-16283	GCA_000716975.1	2055	2055	suspected-type	True	100.0	1857	1858	95	conclusive
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	99.9967	1856	1858	95	conclusive
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	99.9957	1857	1858	95	conclusive
Gordonia terrae	strain=NCTC10669	GCA_901542405.1	2055	2055	suspected-type	True	99.9957	1857	1858	95	conclusive
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	99.9665	1805	1858	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:02:22,929] [INFO] DFAST Taxonomy check result was written to GCF_000716975.1_ASM71697v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:22,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:22,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:22,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference/checkm_data
[2024-01-24 13:02:22,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:23,004] [INFO] Task started: CheckM
[2024-01-24 13:02:23,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000716975.1_ASM71697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000716975.1_ASM71697v1_genomic.fna/checkm_input GCF_000716975.1_ASM71697v1_genomic.fna/checkm_result
[2024-01-24 13:03:39,687] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:39,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:39,715] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:39,715] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:39,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000716975.1_ASM71697v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:39,716] [INFO] Task started: Blastn
[2024-01-24 13:03:39,716] [INFO] Running command: blastn -query GCF_000716975.1_ASM71697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9cfa19f-ca2b-45af-bbf2-d126c0054df7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000716975.1_ASM71697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:41,416] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:41,420] [INFO] Selected 7 target genomes.
[2024-01-24 13:03:41,420] [INFO] Target genome list was writen to GCF_000716975.1_ASM71697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:41,424] [INFO] Task started: fastANI
[2024-01-24 13:03:41,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19bbd89-3479-4e55-9483-4e52bea7cb13/GCF_000716975.1_ASM71697v1_genomic.fna.gz --refList GCF_000716975.1_ASM71697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000716975.1_ASM71697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:51,835] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:51,849] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:51,850] [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_001698225.1	s__Gordonia terrae	99.9957	1857	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	conclusive
GCF_002149015.1	s__Gordonia lacunae	91.7458	1582	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143885.2	s__Gordonia sp000143885	89.4995	1505	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCF_011290605.1	s__Gordonia sp002009645	88.869	1476	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCA_014041935.1	s__Gordonia sp014041935	83.1658	1211	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.20	99.20	0.95	0.95	2	-
GCF_900105725.1	s__Gordonia westfalica	83.0821	1262	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327325.1	s__Gordonia rubripertincta	82.9955	1157	1858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:51,852] [INFO] GTDB search result was written to GCF_000716975.1_ASM71697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:51,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:51,858] [INFO] DFAST_QC result json was written to GCF_000716975.1_ASM71697v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:51,858] [INFO] DFAST_QC completed!
[2024-01-24 13:03:51,858] [INFO] Total running time: 0h2m2s