[2024-01-25 19:03:35,755] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:35,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:35,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference
[2024-01-25 19:03:36,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:36,861] [INFO] Task started: Prodigal
[2024-01-25 19:03:36,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg810821ed-1445-4dc9-ac19-bf4ec48c7e50/GCF_017876405.1_ASM1787640v1_genomic.fna.gz | prodigal -d GCF_017876405.1_ASM1787640v1_genomic.fna/cds.fna -a GCF_017876405.1_ASM1787640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:00,128] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:00,129] [INFO] Task started: HMMsearch
[2024-01-25 19:05:00,129] [INFO] Running command: hmmsearch --tblout GCF_017876405.1_ASM1787640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference/reference_markers.hmm GCF_017876405.1_ASM1787640v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:00,561] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:00,563] [INFO] Found 6/6 markers.
[2024-01-25 19:05:00,653] [INFO] Query marker FASTA was written to GCF_017876405.1_ASM1787640v1_genomic.fna/markers.fasta
[2024-01-25 19:05:00,653] [INFO] Task started: Blastn
[2024-01-25 19:05:00,653] [INFO] Running command: blastn -query GCF_017876405.1_ASM1787640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference/reference_markers.fasta -out GCF_017876405.1_ASM1787640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:01,821] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:01,824] [INFO] Selected 10 target genomes.
[2024-01-25 19:05:01,824] [INFO] Target genome list was writen to GCF_017876405.1_ASM1787640v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:01,832] [INFO] Task started: fastANI
[2024-01-25 19:05:01,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg810821ed-1445-4dc9-ac19-bf4ec48c7e50/GCF_017876405.1_ASM1787640v1_genomic.fna.gz --refList GCF_017876405.1_ASM1787640v1_genomic.fna/target_genomes.txt --output GCF_017876405.1_ASM1787640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:26,168] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:26,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:26,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:26,175] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:26,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:26,176] [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
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	100.0	4267	4269	95	conclusive
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	82.6726	1874	4269	95	below_threshold
Kibdelosporangium aridum	strain=DSM 43828	GCA_900176515.1	2030	2030	type	True	82.4541	2127	4269	95	below_threshold
Kibdelosporangium phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	81.9584	1859	4269	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	81.9267	1876	4269	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.3017	839	4269	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	78.0957	1023	4269	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0166	1125	4269	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	77.9104	997	4269	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.8151	757	4269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:26,177] [INFO] DFAST Taxonomy check result was written to GCF_017876405.1_ASM1787640v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:26,177] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:26,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:26,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference/checkm_data
[2024-01-25 19:05:26,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:26,289] [INFO] Task started: CheckM
[2024-01-25 19:05:26,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876405.1_ASM1787640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876405.1_ASM1787640v1_genomic.fna/checkm_input GCF_017876405.1_ASM1787640v1_genomic.fna/checkm_result
[2024-01-25 19:11:48,520] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:48,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:48,575] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:48,575] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:48,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876405.1_ASM1787640v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:48,577] [INFO] Task started: Blastn
[2024-01-25 19:11:48,577] [INFO] Running command: blastn -query GCF_017876405.1_ASM1787640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64023035-b9fa-4aec-be36-2eef80ac43d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876405.1_ASM1787640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:50,392] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:50,395] [INFO] Selected 7 target genomes.
[2024-01-25 19:11:50,395] [INFO] Target genome list was writen to GCF_017876405.1_ASM1787640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:50,420] [INFO] Task started: fastANI
[2024-01-25 19:11:50,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg810821ed-1445-4dc9-ac19-bf4ec48c7e50/GCF_017876405.1_ASM1787640v1_genomic.fna.gz --refList GCF_017876405.1_ASM1787640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876405.1_ASM1787640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:12,270] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:12,276] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:12,276] [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_017876405.1	s__Kibdelosporangium banguiense	100.0	4267	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013280595.1	s__Kibdelosporangium persicum	82.6732	1876	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720375.1	s__Kibdelosporangium sp000720375	82.5432	2140	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900176515.1	s__Kibdelosporangium aridum	82.4274	2133	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826545.1	s__Kibdelosporangium sp000826545	82.003	1806	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302585.1	s__Kibdelosporangium phytohabitans	81.9444	1862	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001984155.1	s__Kibdelosporangium sp001984155	81.8998	1837	4269	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:12,278] [INFO] GTDB search result was written to GCF_017876405.1_ASM1787640v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:12,279] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:12,282] [INFO] DFAST_QC result json was written to GCF_017876405.1_ASM1787640v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:12,282] [INFO] DFAST_QC completed!
[2024-01-25 19:12:12,282] [INFO] Total running time: 0h8m37s