[2024-01-24 13:58:11,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,300] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference
[2024-01-24 13:58:12,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,635] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,635] [INFO] Running command: gunzip -c /var/lib/cwl/stge7d6fdad-4ab3-4765-9e4e-21cb8625b589/GCF_000239155.1_ASM23915v2_genomic.fna.gz | prodigal -d GCF_000239155.1_ASM23915v2_genomic.fna/cds.fna -a GCF_000239155.1_ASM23915v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:26,614] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:26,614] [INFO] Task started: HMMsearch
[2024-01-24 13:58:26,614] [INFO] Running command: hmmsearch --tblout GCF_000239155.1_ASM23915v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference/reference_markers.hmm GCF_000239155.1_ASM23915v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:26,968] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:26,970] [INFO] Found 6/6 markers.
[2024-01-24 13:58:27,031] [INFO] Query marker FASTA was written to GCF_000239155.1_ASM23915v2_genomic.fna/markers.fasta
[2024-01-24 13:58:27,031] [INFO] Task started: Blastn
[2024-01-24 13:58:27,031] [INFO] Running command: blastn -query GCF_000239155.1_ASM23915v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference/reference_markers.fasta -out GCF_000239155.1_ASM23915v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:28,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:28,406] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:28,406] [INFO] Target genome list was writen to GCF_000239155.1_ASM23915v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:28,471] [INFO] Task started: fastANI
[2024-01-24 13:58:28,471] [INFO] Running command: fastANI --query /var/lib/cwl/stge7d6fdad-4ab3-4765-9e4e-21cb8625b589/GCF_000239155.1_ASM23915v2_genomic.fna.gz --refList GCF_000239155.1_ASM23915v2_genomic.fna/target_genomes.txt --output GCF_000239155.1_ASM23915v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:53,370] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:53,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:53,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:53,387] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:53,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:53,388] [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
Actinoalloteichus spitiensis	strain=RMV-1378	GCA_000239155.2	252394	252394	type	True	100.0	1457	1483	95	conclusive
Actinoalloteichus cyanogriseus	strain=DSM 43889	GCA_000429185.2	65497	65497	type	True	92.6271	1352	1483	95	below_threshold
Actinoalloteichus fjordicus	strain=ADI127-7	GCA_001941625.1	1612552	1612552	type	True	78.6205	556	1483	95	below_threshold
Actinoalloteichus hymeniacidonis	strain=DSM 45092	GCA_014203365.1	340345	340345	type	True	78.4043	483	1483	95	below_threshold
Actinoalloteichus hoggarensis	strain=DSM 45943	GCA_002234535.1	1470176	1470176	type	True	78.3826	579	1483	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	78.301	529	1483	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	78.2231	426	1483	95	below_threshold
Saccharopolyspora antimicrobica	strain=DSM 45119	GCA_003635025.1	455193	455193	type	True	78.1516	482	1483	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	78.0864	538	1483	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	78.0569	523	1483	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	78.0522	512	1483	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	78.0103	514	1483	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.5889	457	1483	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	77.5882	465	1483	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	77.5701	536	1483	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.375	432	1483	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	77.0652	499	1483	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.041	488	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,389] [INFO] DFAST Taxonomy check result was written to GCF_000239155.1_ASM23915v2_genomic.fna/tc_result.tsv
[2024-01-24 13:58:53,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:53,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:53,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference/checkm_data
[2024-01-24 13:58:53,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:53,449] [INFO] Task started: CheckM
[2024-01-24 13:58:53,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000239155.1_ASM23915v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000239155.1_ASM23915v2_genomic.fna/checkm_input GCF_000239155.1_ASM23915v2_genomic.fna/checkm_result
[2024-01-24 13:59:38,556] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:38,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:38,579] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:38,579] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:38,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000239155.1_ASM23915v2_genomic.fna/markers.fasta)
[2024-01-24 13:59:38,580] [INFO] Task started: Blastn
[2024-01-24 13:59:38,580] [INFO] Running command: blastn -query GCF_000239155.1_ASM23915v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8fb66f0a-fe57-4406-a654-f4020f3d06fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000239155.1_ASM23915v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:40,365] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:40,367] [INFO] Selected 18 target genomes.
[2024-01-24 13:59:40,368] [INFO] Target genome list was writen to GCF_000239155.1_ASM23915v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:40,384] [INFO] Task started: fastANI
[2024-01-24 13:59:40,384] [INFO] Running command: fastANI --query /var/lib/cwl/stge7d6fdad-4ab3-4765-9e4e-21cb8625b589/GCF_000239155.1_ASM23915v2_genomic.fna.gz --refList GCF_000239155.1_ASM23915v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000239155.1_ASM23915v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:03,327] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:03,342] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:03,342] [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_000239155.1	s__Actinoalloteichus spitiensis	100.0	1457	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000429185.1	s__Actinoalloteichus cyanogriseus	92.6222	1348	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.50	99.47	0.98	0.97	3	-
GCF_001941625.1	s__Actinoalloteichus fjordicus	78.6204	556	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	99.71	99.71	0.98	0.98	2	-
GCF_002234535.1	s__Actinoalloteichus hoggarensis	78.3945	577	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001747425.1	s__Actinoalloteichus hymeniacidonis	78.3367	482	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinoalloteichus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	78.3271	526	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	78.3125	426	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646075.1	s__Saccharopolyspora subtropica	78.2227	426	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003635025.1	s__Saccharopolyspora antimicrobica	78.1174	485	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	96.3257	100.00	100.00	1.00	1.00	2	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	78.0813	520	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	78.0184	517	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	77.9431	590	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	77.7472	532	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203355.1	s__Kutzneria kofuensis	77.5494	534	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	77.5088	476	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	77.4157	493	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429145.1	s__Amycolatopsis sp009429145	77.3845	503	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364325.1	s__Actinophytocola oryzae	77.0493	503	1483	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:03,343] [INFO] GTDB search result was written to GCF_000239155.1_ASM23915v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:03,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:03,348] [INFO] DFAST_QC result json was written to GCF_000239155.1_ASM23915v2_genomic.fna/dqc_result.json
[2024-01-24 14:00:03,348] [INFO] DFAST_QC completed!
[2024-01-24 14:00:03,348] [INFO] Total running time: 0h1m52s