[2024-01-25 19:04:50,511] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:50,512] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:50,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference
[2024-01-25 19:04:51,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:51,670] [INFO] Task started: Prodigal
[2024-01-25 19:04:51,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg65fed80b-f811-49b9-a85a-40bad28955b8/GCF_024171945.1_ASM2417194v1_genomic.fna.gz | prodigal -d GCF_024171945.1_ASM2417194v1_genomic.fna/cds.fna -a GCF_024171945.1_ASM2417194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:13,237] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:13,237] [INFO] Task started: HMMsearch
[2024-01-25 19:05:13,238] [INFO] Running command: hmmsearch --tblout GCF_024171945.1_ASM2417194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference/reference_markers.hmm GCF_024171945.1_ASM2417194v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:13,548] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:13,549] [INFO] Found 6/6 markers.
[2024-01-25 19:05:13,610] [INFO] Query marker FASTA was written to GCF_024171945.1_ASM2417194v1_genomic.fna/markers.fasta
[2024-01-25 19:05:13,610] [INFO] Task started: Blastn
[2024-01-25 19:05:13,610] [INFO] Running command: blastn -query GCF_024171945.1_ASM2417194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference/reference_markers.fasta -out GCF_024171945.1_ASM2417194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:14,852] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:14,855] [INFO] Selected 10 target genomes.
[2024-01-25 19:05:14,855] [INFO] Target genome list was writen to GCF_024171945.1_ASM2417194v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:14,865] [INFO] Task started: fastANI
[2024-01-25 19:05:14,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fed80b-f811-49b9-a85a-40bad28955b8/GCF_024171945.1_ASM2417194v1_genomic.fna.gz --refList GCF_024171945.1_ASM2417194v1_genomic.fna/target_genomes.txt --output GCF_024171945.1_ASM2417194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:35,813] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:35,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:35,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:35,822] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:35,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:35,822] [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
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	100.0	2540	2540	95	conclusive
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	89.7577	2046	2540	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	89.6731	2010	2540	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	86.8323	1876	2540	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	86.7082	1827	2540	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	83.3068	1555	2540	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	82.2608	1131	2540	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.5719	852	2540	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	77.9199	784	2540	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	76.5625	651	2540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:35,824] [INFO] DFAST Taxonomy check result was written to GCF_024171945.1_ASM2417194v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:35,825] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:35,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:35,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference/checkm_data
[2024-01-25 19:05:35,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:35,896] [INFO] Task started: CheckM
[2024-01-25 19:05:35,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171945.1_ASM2417194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171945.1_ASM2417194v1_genomic.fna/checkm_input GCF_024171945.1_ASM2417194v1_genomic.fna/checkm_result
[2024-01-25 19:07:07,495] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:07,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:07,521] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:07,521] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:07,522] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171945.1_ASM2417194v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:07,522] [INFO] Task started: Blastn
[2024-01-25 19:07:07,522] [INFO] Running command: blastn -query GCF_024171945.1_ASM2417194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaab11fa8-b5de-4b05-b420-17da24197d93/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171945.1_ASM2417194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:09,489] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:09,491] [INFO] Selected 12 target genomes.
[2024-01-25 19:07:09,492] [INFO] Target genome list was writen to GCF_024171945.1_ASM2417194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:09,501] [INFO] Task started: fastANI
[2024-01-25 19:07:09,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fed80b-f811-49b9-a85a-40bad28955b8/GCF_024171945.1_ASM2417194v1_genomic.fna.gz --refList GCF_024171945.1_ASM2417194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171945.1_ASM2417194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:31,957] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:31,965] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:07:31,965] [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_900111175.1	s__Actinokineospora terrae	89.7756	2043	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_016907695.1	s__Actinokineospora baliensis	86.6943	1829	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	84.2814	1560	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	83.3121	1555	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	83.0332	1433	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	82.2458	1134	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323725.1	s__Actinokineospora xionganensis	81.0982	1057	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	79.0179	853	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	78.8321	876	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	78.5253	928	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	78.4608	958	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000194155.1	s__Saccharopolyspora spinosa	78.2238	658	2540	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	99.78	99.78	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:31,968] [INFO] GTDB search result was written to GCF_024171945.1_ASM2417194v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:31,968] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:31,971] [INFO] DFAST_QC result json was written to GCF_024171945.1_ASM2417194v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:31,971] [INFO] DFAST_QC completed!
[2024-01-25 19:07:31,971] [INFO] Total running time: 0h2m41s