[2024-01-24 11:12:57,910] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:57,912] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:57,912] [INFO] DQC Reference Directory: /var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference
[2024-01-24 11:12:59,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,327] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg220d6c71-93ee-4e47-bdb3-167611c58e63/GCF_014873115.1_ASM1487311v1_genomic.fna.gz | prodigal -d GCF_014873115.1_ASM1487311v1_genomic.fna/cds.fna -a GCF_014873115.1_ASM1487311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:03,003] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:03,004] [INFO] Task started: HMMsearch
[2024-01-24 11:14:03,004] [INFO] Running command: hmmsearch --tblout GCF_014873115.1_ASM1487311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference/reference_markers.hmm GCF_014873115.1_ASM1487311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:03,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:03,478] [INFO] Found 6/6 markers.
[2024-01-24 11:14:03,569] [INFO] Query marker FASTA was written to GCF_014873115.1_ASM1487311v1_genomic.fna/markers.fasta
[2024-01-24 11:14:03,570] [INFO] Task started: Blastn
[2024-01-24 11:14:03,570] [INFO] Running command: blastn -query GCF_014873115.1_ASM1487311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference/reference_markers.fasta -out GCF_014873115.1_ASM1487311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:04,837] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:04,841] [INFO] Selected 9 target genomes.
[2024-01-24 11:14:04,841] [INFO] Target genome list was writen to GCF_014873115.1_ASM1487311v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:04,845] [INFO] Task started: fastANI
[2024-01-24 11:14:04,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg220d6c71-93ee-4e47-bdb3-167611c58e63/GCF_014873115.1_ASM1487311v1_genomic.fna.gz --refList GCF_014873115.1_ASM1487311v1_genomic.fna/target_genomes.txt --output GCF_014873115.1_ASM1487311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:26,844] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:26,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:26,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:26,855] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:26,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:26,855] [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 phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	99.9979	3903	3918	95	conclusive
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	84.8118	2104	3918	95	below_threshold
Kibdelosporangium aridum	strain=DSM 43828	GCA_900176515.1	2030	2030	type	True	84.0207	2254	3918	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	83.3444	2038	3918	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	81.8571	1871	3918	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.5121	961	3918	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.3012	955	3918	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9453	1210	3918	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.825	887	3918	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:26,858] [INFO] DFAST Taxonomy check result was written to GCF_014873115.1_ASM1487311v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:26,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:26,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:26,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference/checkm_data
[2024-01-24 11:14:26,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:26,961] [INFO] Task started: CheckM
[2024-01-24 11:14:26,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873115.1_ASM1487311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873115.1_ASM1487311v1_genomic.fna/checkm_input GCF_014873115.1_ASM1487311v1_genomic.fna/checkm_result
[2024-01-24 11:19:04,257] [INFO] Task succeeded: CheckM
[2024-01-24 11:19:04,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:19:04,284] [INFO] ===== Completeness check finished =====
[2024-01-24 11:19:04,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:19:04,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873115.1_ASM1487311v1_genomic.fna/markers.fasta)
[2024-01-24 11:19:04,286] [INFO] Task started: Blastn
[2024-01-24 11:19:04,286] [INFO] Running command: blastn -query GCF_014873115.1_ASM1487311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga406ea54-888f-47d5-9cb1-16bcce6e7893/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873115.1_ASM1487311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:06,213] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:06,218] [INFO] Selected 7 target genomes.
[2024-01-24 11:19:06,218] [INFO] Target genome list was writen to GCF_014873115.1_ASM1487311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:19:06,295] [INFO] Task started: fastANI
[2024-01-24 11:19:06,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg220d6c71-93ee-4e47-bdb3-167611c58e63/GCF_014873115.1_ASM1487311v1_genomic.fna.gz --refList GCF_014873115.1_ASM1487311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873115.1_ASM1487311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:19:26,566] [INFO] Task succeeded: fastANI
[2024-01-24 11:19:26,586] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:19:26,586] [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_001302585.1	s__Kibdelosporangium phytohabitans	99.9979	3902	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001984155.1	s__Kibdelosporangium sp001984155	89.166	2802	3918	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	87.0109	2657	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013280595.1	s__Kibdelosporangium persicum	84.7599	2108	3918	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	84.1096	2208	3918	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	84.0167	2256	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942305.1	s__Saccharomonospora sp001942305	77.677	622	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:19:26,588] [INFO] GTDB search result was written to GCF_014873115.1_ASM1487311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:19:26,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:19:26,594] [INFO] DFAST_QC result json was written to GCF_014873115.1_ASM1487311v1_genomic.fna/dqc_result.json
[2024-01-24 11:19:26,594] [INFO] DFAST_QC completed!
[2024-01-24 11:19:26,595] [INFO] Total running time: 0h6m29s