[2024-01-24 11:05:24,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference
[2024-01-24 11:05:26,404] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,405] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg60c93a1f-7fe4-4449-9325-45a5a309cf6f/GCF_014874035.1_ASM1487403v1_genomic.fna.gz | prodigal -d GCF_014874035.1_ASM1487403v1_genomic.fna/cds.fna -a GCF_014874035.1_ASM1487403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:44,228] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:44,228] [INFO] Task started: HMMsearch
[2024-01-24 11:05:44,229] [INFO] Running command: hmmsearch --tblout GCF_014874035.1_ASM1487403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference/reference_markers.hmm GCF_014874035.1_ASM1487403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:44,551] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:44,552] [INFO] Found 6/6 markers.
[2024-01-24 11:05:44,601] [INFO] Query marker FASTA was written to GCF_014874035.1_ASM1487403v1_genomic.fna/markers.fasta
[2024-01-24 11:05:44,602] [INFO] Task started: Blastn
[2024-01-24 11:05:44,602] [INFO] Running command: blastn -query GCF_014874035.1_ASM1487403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference/reference_markers.fasta -out GCF_014874035.1_ASM1487403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:45,898] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:45,901] [INFO] Selected 12 target genomes.
[2024-01-24 11:05:45,901] [INFO] Target genome list was writen to GCF_014874035.1_ASM1487403v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:45,906] [INFO] Task started: fastANI
[2024-01-24 11:05:45,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c93a1f-7fe4-4449-9325-45a5a309cf6f/GCF_014874035.1_ASM1487403v1_genomic.fna.gz --refList GCF_014874035.1_ASM1487403v1_genomic.fna/target_genomes.txt --output GCF_014874035.1_ASM1487403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:03,998] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:03,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:03,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:04,014] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:04,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:04,015] [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
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	100.0	2011	2012	95	conclusive
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	99.9894	1990	2012	95	conclusive
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	88.5827	1581	2012	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	87.8623	1568	2012	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	87.7761	1572	2012	95	below_threshold
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	87.6868	1558	2012	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	86.5963	1348	2012	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.9347	1319	2012	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	83.6303	1194	2012	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.43	988	2012	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.4876	715	2012	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.348	769	2012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:04,020] [INFO] DFAST Taxonomy check result was written to GCF_014874035.1_ASM1487403v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:04,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:04,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:04,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference/checkm_data
[2024-01-24 11:06:04,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:04,082] [INFO] Task started: CheckM
[2024-01-24 11:06:04,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014874035.1_ASM1487403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014874035.1_ASM1487403v1_genomic.fna/checkm_input GCF_014874035.1_ASM1487403v1_genomic.fna/checkm_result
[2024-01-24 11:07:08,323] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:08,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:08,346] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:08,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:08,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014874035.1_ASM1487403v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:08,347] [INFO] Task started: Blastn
[2024-01-24 11:07:08,347] [INFO] Running command: blastn -query GCF_014874035.1_ASM1487403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e7796c3-e137-4ea5-aa52-72de80deaa21/dqc_reference/reference_markers_gtdb.fasta -out GCF_014874035.1_ASM1487403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:10,377] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:10,381] [INFO] Selected 11 target genomes.
[2024-01-24 11:07:10,381] [INFO] Target genome list was writen to GCF_014874035.1_ASM1487403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:10,405] [INFO] Task started: fastANI
[2024-01-24 11:07:10,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c93a1f-7fe4-4449-9325-45a5a309cf6f/GCF_014874035.1_ASM1487403v1_genomic.fna.gz --refList GCF_014874035.1_ASM1487403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014874035.1_ASM1487403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:27,894] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:27,906] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:27,907] [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_014651695.1	s__Nocardiopsis terrae	99.9894	1990	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000341085.1	s__Nocardiopsis ganjiahuensis	88.5988	1579	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	87.7724	1574	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340985.1	s__Nocardiopsis valliformis	87.7075	1556	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341265.1	s__Nocardiopsis prasina	86.6504	1341	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCA_018388625.1	s__Nocardiopsis sp018388625	86.5411	1388	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018207095.1	s__Nocardiopsis sp018207095	84.5826	1240	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341225.1	s__Nocardiopsis alba	84.472	1262	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	98.86	98.56	0.95	0.95	4	-
GCF_001905145.1	s__Nocardiopsis sp001905145	84.0609	1299	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	83.8574	1262	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	83.729	1322	2012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:27,908] [INFO] GTDB search result was written to GCF_014874035.1_ASM1487403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:27,909] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:27,912] [INFO] DFAST_QC result json was written to GCF_014874035.1_ASM1487403v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:27,912] [INFO] DFAST_QC completed!
[2024-01-24 11:07:27,912] [INFO] Total running time: 0h2m3s