[2024-01-25 19:50:20,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:20,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:20,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference
[2024-01-25 19:50:21,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:21,661] [INFO] Task started: Prodigal
[2024-01-25 19:50:21,662] [INFO] Running command: gunzip -c /var/lib/cwl/stgc442780e-6a05-440c-a639-4077754738b6/GCF_016862475.1_ASM1686247v1_genomic.fna.gz | prodigal -d GCF_016862475.1_ASM1686247v1_genomic.fna/cds.fna -a GCF_016862475.1_ASM1686247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:48,256] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:48,257] [INFO] Task started: HMMsearch
[2024-01-25 19:50:48,257] [INFO] Running command: hmmsearch --tblout GCF_016862475.1_ASM1686247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference/reference_markers.hmm GCF_016862475.1_ASM1686247v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:48,649] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:48,650] [INFO] Found 6/6 markers.
[2024-01-25 19:50:48,735] [INFO] Query marker FASTA was written to GCF_016862475.1_ASM1686247v1_genomic.fna/markers.fasta
[2024-01-25 19:50:48,735] [INFO] Task started: Blastn
[2024-01-25 19:50:48,735] [INFO] Running command: blastn -query GCF_016862475.1_ASM1686247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference/reference_markers.fasta -out GCF_016862475.1_ASM1686247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:49,975] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:49,988] [INFO] Selected 18 target genomes.
[2024-01-25 19:50:49,989] [INFO] Target genome list was writen to GCF_016862475.1_ASM1686247v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:50,028] [INFO] Task started: fastANI
[2024-01-25 19:50:50,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgc442780e-6a05-440c-a639-4077754738b6/GCF_016862475.1_ASM1686247v1_genomic.fna.gz --refList GCF_016862475.1_ASM1686247v1_genomic.fna/target_genomes.txt --output GCF_016862475.1_ASM1686247v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:39,308] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:39,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:39,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:39,320] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:39,320] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:39,320] [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 xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	99.9989	3498	3505	95	conclusive
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	89.1567	2609	3505	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	89.1126	2568	3505	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	86.2487	2428	3505	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	86.2178	2400	3505	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	85.2309	2100	3505	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	85.0358	2080	3505	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	84.9563	2113	3505	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.9088	2098	3505	95	below_threshold
Actinoplanes derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	84.176	2095	3505	95	below_threshold
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	84.1329	2137	3505	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	82.9434	1871	3505	95	below_threshold
Actinoplanes lutulentus	strain=CGMCC 4.7090	GCA_003259845.1	1287878	1287878	type	True	82.5471	1880	3505	95	below_threshold
Actinoplanes lutulentus	strain=DSM 45883	GCA_014191235.1	1287878	1287878	type	True	82.5163	1844	3505	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.7452	984	3505	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4632	1405	3505	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.2888	1079	3505	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1138	1227	3505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:39,321] [INFO] DFAST Taxonomy check result was written to GCF_016862475.1_ASM1686247v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:39,322] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:39,322] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:39,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference/checkm_data
[2024-01-25 19:51:39,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:39,424] [INFO] Task started: CheckM
[2024-01-25 19:51:39,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862475.1_ASM1686247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862475.1_ASM1686247v1_genomic.fna/checkm_input GCF_016862475.1_ASM1686247v1_genomic.fna/checkm_result
[2024-01-25 19:53:31,913] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:31,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:31,935] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:31,935] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:31,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862475.1_ASM1686247v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:31,937] [INFO] Task started: Blastn
[2024-01-25 19:53:31,937] [INFO] Running command: blastn -query GCF_016862475.1_ASM1686247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36ab0426-8927-4f20-ac8e-48b08774dba0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862475.1_ASM1686247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:33,727] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:33,729] [INFO] Selected 13 target genomes.
[2024-01-25 19:53:33,729] [INFO] Target genome list was writen to GCF_016862475.1_ASM1686247v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:33,744] [INFO] Task started: fastANI
[2024-01-25 19:53:33,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgc442780e-6a05-440c-a639-4077754738b6/GCF_016862475.1_ASM1686247v1_genomic.fna.gz --refList GCF_016862475.1_ASM1686247v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862475.1_ASM1686247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:10,225] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:10,234] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:10,234] [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_003148685.1	s__Actinoplanes xinjiangensis	99.9989	3498	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900113015.1	s__Actinoplanes philippinensis	89.1396	2612	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003001815.1	s__Actinoplanes italicus	86.2258	2434	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016862455.1	s__Actinoplanes utahensis	85.2137	2104	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014647795.1	s__Actinoplanes campanulatus	84.9648	2136	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_017592555.1	s__Actinoplanes sp017592555	84.9235	2093	3505	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	84.9092	2175	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_900104725.1	s__Actinoplanes derwentensis	84.1477	2133	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862075.1	s__Actinoplanes couchii	84.0861	2139	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	82.9662	1866	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259845.1	s__Actinoplanes lutulentus	82.5423	1881	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000962825.1	s__Actinoplanes rectilineatus	82.4275	1796	3505	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	82.4245	1633	3505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:10,236] [INFO] GTDB search result was written to GCF_016862475.1_ASM1686247v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:10,236] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:10,239] [INFO] DFAST_QC result json was written to GCF_016862475.1_ASM1686247v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:10,240] [INFO] DFAST_QC completed!
[2024-01-25 19:54:10,240] [INFO] Total running time: 0h3m50s