[2024-01-24 11:51:25,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:25,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:25,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference
[2024-01-24 11:51:26,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,459] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg35d4883c-2cee-4664-9a25-5d346768b122/GCF_003259845.1_ASM325984v1_genomic.fna.gz | prodigal -d GCF_003259845.1_ASM325984v1_genomic.fna/cds.fna -a GCF_003259845.1_ASM325984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:54,309] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:54,310] [INFO] Task started: HMMsearch
[2024-01-24 11:51:54,310] [INFO] Running command: hmmsearch --tblout GCF_003259845.1_ASM325984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference/reference_markers.hmm GCF_003259845.1_ASM325984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:54,717] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:54,719] [INFO] Found 6/6 markers.
[2024-01-24 11:51:54,794] [INFO] Query marker FASTA was written to GCF_003259845.1_ASM325984v1_genomic.fna/markers.fasta
[2024-01-24 11:51:54,794] [INFO] Task started: Blastn
[2024-01-24 11:51:54,794] [INFO] Running command: blastn -query GCF_003259845.1_ASM325984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference/reference_markers.fasta -out GCF_003259845.1_ASM325984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:56,091] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:56,095] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:56,096] [INFO] Target genome list was writen to GCF_003259845.1_ASM325984v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:56,105] [INFO] Task started: fastANI
[2024-01-24 11:51:56,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg35d4883c-2cee-4664-9a25-5d346768b122/GCF_003259845.1_ASM325984v1_genomic.fna.gz --refList GCF_003259845.1_ASM325984v1_genomic.fna/target_genomes.txt --output GCF_003259845.1_ASM325984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:35,653] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:35,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:35,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:35,668] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:35,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:35,668] [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
Actinoplanes lutulentus	strain=CGMCC 4.7090	GCA_003259845.1	1287878	1287878	type	True	100.0	3270	3273	95	conclusive
Actinoplanes lutulentus	strain=DSM 45883	GCA_014191235.1	1287878	1287878	type	True	99.9846	3229	3273	95	conclusive
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	86.2081	2139	3273	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	82.7093	1865	3273	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	82.7074	1840	3273	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	82.7038	1794	3273	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.6993	1786	3273	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	82.4009	1888	3273	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	82.3704	1534	3273	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	82.3397	1592	3273	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	82.3233	1792	3273	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	82.1265	1706	3273	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	82.0907	1713	3273	95	below_threshold
Actinoplanes regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	82.0763	1696	3273	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.6235	1060	3273	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.5171	888	3273	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4816	833	3273	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1833	1051	3273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:35,670] [INFO] DFAST Taxonomy check result was written to GCF_003259845.1_ASM325984v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:35,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:35,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:35,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference/checkm_data
[2024-01-24 11:52:35,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:35,766] [INFO] Task started: CheckM
[2024-01-24 11:52:35,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259845.1_ASM325984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259845.1_ASM325984v1_genomic.fna/checkm_input GCF_003259845.1_ASM325984v1_genomic.fna/checkm_result
[2024-01-24 11:53:56,216] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:56,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:56,246] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:56,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:56,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259845.1_ASM325984v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:56,247] [INFO] Task started: Blastn
[2024-01-24 11:53:56,247] [INFO] Running command: blastn -query GCF_003259845.1_ASM325984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524efe1b-6398-4350-8f3e-883494e05cb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259845.1_ASM325984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:57,952] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:57,955] [INFO] Selected 14 target genomes.
[2024-01-24 11:53:57,955] [INFO] Target genome list was writen to GCF_003259845.1_ASM325984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:57,965] [INFO] Task started: fastANI
[2024-01-24 11:53:57,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg35d4883c-2cee-4664-9a25-5d346768b122/GCF_003259845.1_ASM325984v1_genomic.fna.gz --refList GCF_003259845.1_ASM325984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259845.1_ASM325984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:31,789] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:31,804] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:31,805] [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_003259845.1	s__Actinoplanes lutulentus	100.0	3270	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000284295.1	s__Actinoplanes missouriensis	86.1629	2148	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001265.1	s__Actinoplanes sp004001265	85.7705	2269	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015704865.1	s__Actinoplanes sp015704865	83.4346	1904	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205215.1	s__Actinoplanes lobatus	82.7214	1882	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_017592555.1	s__Actinoplanes sp017592555	82.6857	1791	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	82.5053	1907	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_000962825.1	s__Actinoplanes rectilineatus	82.4615	1781	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	82.4286	1502	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001815.1	s__Actinoplanes italicus	82.3693	1957	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	82.3617	1898	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	82.3167	1599	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862075.1	s__Actinoplanes couchii	82.2028	1845	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	82.1032	1710	3273	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:31,806] [INFO] GTDB search result was written to GCF_003259845.1_ASM325984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:31,807] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:31,811] [INFO] DFAST_QC result json was written to GCF_003259845.1_ASM325984v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:31,811] [INFO] DFAST_QC completed!
[2024-01-24 11:54:31,811] [INFO] Total running time: 0h3m7s