[2024-01-24 12:09:05,631] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference
[2024-01-24 12:09:06,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,836] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg525ec782-06df-4f37-a9ae-e710f471df93/GCF_004345645.1_ASM434564v1_genomic.fna.gz | prodigal -d GCF_004345645.1_ASM434564v1_genomic.fna/cds.fna -a GCF_004345645.1_ASM434564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:52,784] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:52,785] [INFO] Task started: HMMsearch
[2024-01-24 12:09:52,785] [INFO] Running command: hmmsearch --tblout GCF_004345645.1_ASM434564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference/reference_markers.hmm GCF_004345645.1_ASM434564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:53,226] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:53,227] [INFO] Found 6/6 markers.
[2024-01-24 12:09:53,313] [INFO] Query marker FASTA was written to GCF_004345645.1_ASM434564v1_genomic.fna/markers.fasta
[2024-01-24 12:09:53,314] [INFO] Task started: Blastn
[2024-01-24 12:09:53,314] [INFO] Running command: blastn -query GCF_004345645.1_ASM434564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference/reference_markers.fasta -out GCF_004345645.1_ASM434564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:54,430] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:54,434] [INFO] Selected 13 target genomes.
[2024-01-24 12:09:54,434] [INFO] Target genome list was writen to GCF_004345645.1_ASM434564v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:54,439] [INFO] Task started: fastANI
[2024-01-24 12:09:54,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg525ec782-06df-4f37-a9ae-e710f471df93/GCF_004345645.1_ASM434564v1_genomic.fna.gz --refList GCF_004345645.1_ASM434564v1_genomic.fna/target_genomes.txt --output GCF_004345645.1_ASM434564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:10:20,427] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:20,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:10:20,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:10:20,444] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:10:20,444] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:10:20,444] [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 persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	81.0362	1568	3982	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	80.8271	1636	3982	95	below_threshold
Kibdelosporangium phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	80.6737	1688	3982	95	below_threshold
Kibdelosporangium aridum	strain=DSM 43828	GCA_900176515.1	2030	2030	type	True	80.5017	1587	3982	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	80.1393	1478	3982	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	78.2887	830	3982	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	78.2528	886	3982	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.2024	899	3982	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.0747	926	3982	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	77.8349	931	3982	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	77.7266	1128	3982	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.7242	1210	3982	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.6047	897	3982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:10:20,445] [INFO] DFAST Taxonomy check result was written to GCF_004345645.1_ASM434564v1_genomic.fna/tc_result.tsv
[2024-01-24 12:10:20,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:10:20,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:10:20,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference/checkm_data
[2024-01-24 12:10:20,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:10:20,547] [INFO] Task started: CheckM
[2024-01-24 12:10:20,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345645.1_ASM434564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345645.1_ASM434564v1_genomic.fna/checkm_input GCF_004345645.1_ASM434564v1_genomic.fna/checkm_result
[2024-01-24 12:13:15,692] [INFO] Task succeeded: CheckM
[2024-01-24 12:13:15,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:13:15,721] [INFO] ===== Completeness check finished =====
[2024-01-24 12:13:15,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:13:15,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345645.1_ASM434564v1_genomic.fna/markers.fasta)
[2024-01-24 12:13:15,723] [INFO] Task started: Blastn
[2024-01-24 12:13:15,723] [INFO] Running command: blastn -query GCF_004345645.1_ASM434564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d8b4fab-e64c-46c3-b172-7c1ffa64f33e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345645.1_ASM434564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:17,385] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:17,389] [INFO] Selected 11 target genomes.
[2024-01-24 12:13:17,389] [INFO] Target genome list was writen to GCF_004345645.1_ASM434564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:13:17,537] [INFO] Task started: fastANI
[2024-01-24 12:13:17,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg525ec782-06df-4f37-a9ae-e710f471df93/GCF_004345645.1_ASM434564v1_genomic.fna.gz --refList GCF_004345645.1_ASM434564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345645.1_ASM434564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:13:43,973] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:43,985] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:13:43,985] [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_004345645.1	s__Actinocrispum wychmicini	100.0	3979	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinocrispum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013280595.1	s__Kibdelosporangium persicum	81.0575	1564	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876405.1	s__Kibdelosporangium banguiense	80.8484	1629	3982	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	80.7485	1634	3982	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	80.685	1688	3982	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	80.682	1664	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176515.1	s__Kibdelosporangium aridum	80.4793	1591	3982	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	80.4601	1616	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900101685.1	s__Actinokineospora iranica	78.2954	825	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	77.9277	1101	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	77.8512	1147	3982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:13:43,987] [INFO] GTDB search result was written to GCF_004345645.1_ASM434564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:13:43,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:13:43,993] [INFO] DFAST_QC result json was written to GCF_004345645.1_ASM434564v1_genomic.fna/dqc_result.json
[2024-01-24 12:13:43,993] [INFO] DFAST_QC completed!
[2024-01-24 12:13:43,993] [INFO] Total running time: 0h4m38s