[2024-01-24 13:28:19,328] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,334] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference
[2024-01-24 13:28:20,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,747] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,747] [INFO] Running command: gunzip -c /var/lib/cwl/stgc27214ea-6a53-471d-acd5-7a272eb92c5f/GCF_014137995.1_ASM1413799v1_genomic.fna.gz | prodigal -d GCF_014137995.1_ASM1413799v1_genomic.fna/cds.fna -a GCF_014137995.1_ASM1413799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:39,956] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:39,957] [INFO] Task started: HMMsearch
[2024-01-24 13:28:39,957] [INFO] Running command: hmmsearch --tblout GCF_014137995.1_ASM1413799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference/reference_markers.hmm GCF_014137995.1_ASM1413799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:40,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:40,330] [INFO] Found 6/6 markers.
[2024-01-24 13:28:40,394] [INFO] Query marker FASTA was written to GCF_014137995.1_ASM1413799v1_genomic.fna/markers.fasta
[2024-01-24 13:28:40,395] [INFO] Task started: Blastn
[2024-01-24 13:28:40,395] [INFO] Running command: blastn -query GCF_014137995.1_ASM1413799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference/reference_markers.fasta -out GCF_014137995.1_ASM1413799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:41,777] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:41,784] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:41,785] [INFO] Target genome list was writen to GCF_014137995.1_ASM1413799v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:41,797] [INFO] Task started: fastANI
[2024-01-24 13:28:41,799] [INFO] Running command: fastANI --query /var/lib/cwl/stgc27214ea-6a53-471d-acd5-7a272eb92c5f/GCF_014137995.1_ASM1413799v1_genomic.fna.gz --refList GCF_014137995.1_ASM1413799v1_genomic.fna/target_genomes.txt --output GCF_014137995.1_ASM1413799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:58,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:58,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:58,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:58,921] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:58,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:58,921] [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
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	100.0	2165	2167	95	conclusive
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	89.5341	1434	2167	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	86.6245	1295	2167	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	85.4047	1416	2167	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	85.1305	1206	2167	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	85.0411	1311	2167	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	80.3195	867	2167	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.0756	794	2167	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.3017	627	2167	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.7664	655	2167	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.6876	573	2167	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.5442	689	2167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:58,923] [INFO] DFAST Taxonomy check result was written to GCF_014137995.1_ASM1413799v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:58,923] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:58,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:58,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference/checkm_data
[2024-01-24 13:28:58,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:58,986] [INFO] Task started: CheckM
[2024-01-24 13:28:58,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014137995.1_ASM1413799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014137995.1_ASM1413799v1_genomic.fna/checkm_input GCF_014137995.1_ASM1413799v1_genomic.fna/checkm_result
[2024-01-24 13:30:08,688] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:08,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:08,713] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:08,713] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:08,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014137995.1_ASM1413799v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:08,714] [INFO] Task started: Blastn
[2024-01-24 13:30:08,715] [INFO] Running command: blastn -query GCF_014137995.1_ASM1413799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd13fc9b-ce25-4fbf-8a89-dfe7b840f5e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014137995.1_ASM1413799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:10,888] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:10,896] [INFO] Selected 10 target genomes.
[2024-01-24 13:30:10,896] [INFO] Target genome list was writen to GCF_014137995.1_ASM1413799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:10,913] [INFO] Task started: fastANI
[2024-01-24 13:30:10,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgc27214ea-6a53-471d-acd5-7a272eb92c5f/GCF_014137995.1_ASM1413799v1_genomic.fna.gz --refList GCF_014137995.1_ASM1413799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014137995.1_ASM1413799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:28,114] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:28,125] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:28,125] [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_014137995.1	s__Promicromonospora sukumoe	100.0	2164	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000385135.1	s__Promicromonospora sukumoe_B	90.495	1746	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	89.5195	1435	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
GCF_003058225.1	s__Promicromonospora sp003058225	87.3362	1539	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_003550025.1	s__Promicromonospora thailandica	87.1401	1547	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653785.1	s__Promicromonospora soli	86.611	1297	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900608595.1	s__Promicromonospora panici	86.127	1421	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096495.1	s__Promicromonospora sukumoe_A	86.0984	1450	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	79.3018	817	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	79.2843	818	2167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:28,127] [INFO] GTDB search result was written to GCF_014137995.1_ASM1413799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:28,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:28,142] [INFO] DFAST_QC result json was written to GCF_014137995.1_ASM1413799v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:28,142] [INFO] DFAST_QC completed!
[2024-01-24 13:30:28,143] [INFO] Total running time: 0h2m9s