[2024-01-24 12:54:39,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference
[2024-01-24 12:54:41,311] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:41,312] [INFO] Task started: Prodigal
[2024-01-24 12:54:41,312] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0ac02be-44a1-47c5-8dd9-6415bf3cc0ae/GCF_024171955.1_ASM2417195v1_genomic.fna.gz | prodigal -d GCF_024171955.1_ASM2417195v1_genomic.fna/cds.fna -a GCF_024171955.1_ASM2417195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:56,658] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:56,658] [INFO] Task started: HMMsearch
[2024-01-24 12:54:56,658] [INFO] Running command: hmmsearch --tblout GCF_024171955.1_ASM2417195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference/reference_markers.hmm GCF_024171955.1_ASM2417195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:56,966] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:56,968] [INFO] Found 6/6 markers.
[2024-01-24 12:54:57,013] [INFO] Query marker FASTA was written to GCF_024171955.1_ASM2417195v1_genomic.fna/markers.fasta
[2024-01-24 12:54:57,014] [INFO] Task started: Blastn
[2024-01-24 12:54:57,014] [INFO] Running command: blastn -query GCF_024171955.1_ASM2417195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference/reference_markers.fasta -out GCF_024171955.1_ASM2417195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:58,375] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:58,378] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:58,379] [INFO] Target genome list was writen to GCF_024171955.1_ASM2417195v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:58,384] [INFO] Task started: fastANI
[2024-01-24 12:54:58,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ac02be-44a1-47c5-8dd9-6415bf3cc0ae/GCF_024171955.1_ASM2417195v1_genomic.fna.gz --refList GCF_024171955.1_ASM2417195v1_genomic.fna/target_genomes.txt --output GCF_024171955.1_ASM2417195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:14,001] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:14,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:14,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:14,013] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:55:14,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:55:14,013] [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 citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	87.6433	1281	1781	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	87.5728	1391	1781	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	86.2153	1373	1781	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	85.8383	1232	1781	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	85.1699	1167	1781	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	84.8386	1280	1781	95	below_threshold
Myceligenerans indicum	strain=I2	GCA_016742955.1	2593663	2593663	type	True	79.9355	794	1781	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	79.1993	628	1781	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.0491	518	1781	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.8847	632	1781	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.3979	467	1781	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	76.4973	477	1781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:14,015] [INFO] DFAST Taxonomy check result was written to GCF_024171955.1_ASM2417195v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:14,015] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:14,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:14,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference/checkm_data
[2024-01-24 12:55:14,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:14,072] [INFO] Task started: CheckM
[2024-01-24 12:55:14,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171955.1_ASM2417195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171955.1_ASM2417195v1_genomic.fna/checkm_input GCF_024171955.1_ASM2417195v1_genomic.fna/checkm_result
[2024-01-24 12:56:32,852] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:32,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:32,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:32,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:32,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171955.1_ASM2417195v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:32,876] [INFO] Task started: Blastn
[2024-01-24 12:56:32,877] [INFO] Running command: blastn -query GCF_024171955.1_ASM2417195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72ebedbc-3896-4771-ad55-87987b67dc86/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171955.1_ASM2417195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:34,804] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:34,808] [INFO] Selected 9 target genomes.
[2024-01-24 12:56:34,808] [INFO] Target genome list was writen to GCF_024171955.1_ASM2417195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:34,816] [INFO] Task started: fastANI
[2024-01-24 12:56:34,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ac02be-44a1-47c5-8dd9-6415bf3cc0ae/GCF_024171955.1_ASM2417195v1_genomic.fna.gz --refList GCF_024171955.1_ASM2417195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171955.1_ASM2417195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:48,770] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:48,784] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:56:48,784] [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_003550025.1	s__Promicromonospora thailandica	88.321	1439	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	87.6739	1278	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	86.409	1392	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_014137995.1	s__Promicromonospora sukumoe	86.2034	1375	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	85.8094	1235	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
GCF_900608595.1	s__Promicromonospora panici	85.6162	1291	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	85.5761	1312	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_003096495.1	s__Promicromonospora sukumoe_A	85.3248	1327	1781	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	85.1449	1170	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:48,786] [INFO] GTDB search result was written to GCF_024171955.1_ASM2417195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:48,786] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:48,789] [INFO] DFAST_QC result json was written to GCF_024171955.1_ASM2417195v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:48,790] [INFO] DFAST_QC completed!
[2024-01-24 12:56:48,790] [INFO] Total running time: 0h2m9s