[2024-01-24 11:12:39,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,906] [INFO] DQC Reference Directory: /var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference
[2024-01-24 11:12:41,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,261] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg535a029c-6f03-45e1-96a7-2089bce27149/GCF_019429605.1_ASM1942960v1_genomic.fna.gz | prodigal -d GCF_019429605.1_ASM1942960v1_genomic.fna/cds.fna -a GCF_019429605.1_ASM1942960v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:07,768] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:07,768] [INFO] Task started: HMMsearch
[2024-01-24 11:13:07,768] [INFO] Running command: hmmsearch --tblout GCF_019429605.1_ASM1942960v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference/reference_markers.hmm GCF_019429605.1_ASM1942960v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:08,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:08,155] [INFO] Found 6/6 markers.
[2024-01-24 11:13:08,232] [INFO] Query marker FASTA was written to GCF_019429605.1_ASM1942960v1_genomic.fna/markers.fasta
[2024-01-24 11:13:08,233] [INFO] Task started: Blastn
[2024-01-24 11:13:08,233] [INFO] Running command: blastn -query GCF_019429605.1_ASM1942960v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference/reference_markers.fasta -out GCF_019429605.1_ASM1942960v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:09,472] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:09,475] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:09,475] [INFO] Target genome list was writen to GCF_019429605.1_ASM1942960v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:09,499] [INFO] Task started: fastANI
[2024-01-24 11:13:09,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg535a029c-6f03-45e1-96a7-2089bce27149/GCF_019429605.1_ASM1942960v1_genomic.fna.gz --refList GCF_019429605.1_ASM1942960v1_genomic.fna/target_genomes.txt --output GCF_019429605.1_ASM1942960v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:35,562] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:35,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:35,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:35,579] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:13:35,579] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:13:35,579] [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 hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	100.0	3067	3076	95	inconclusive
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	96.3153	2680	3076	95	inconclusive
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	96.2918	2722	3076	95	inconclusive
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	96.0321	2637	3076	95	inconclusive
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	95.1062	2624	3076	95	inconclusive
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	94.0333	2567	3076	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.1625	823	3076	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.9969	926	3076	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.5086	1346	3076	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.3166	1146	3076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:35,581] [INFO] DFAST Taxonomy check result was written to GCF_019429605.1_ASM1942960v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:35,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:35,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:35,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference/checkm_data
[2024-01-24 11:13:35,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:35,664] [INFO] Task started: CheckM
[2024-01-24 11:13:35,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019429605.1_ASM1942960v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019429605.1_ASM1942960v1_genomic.fna/checkm_input GCF_019429605.1_ASM1942960v1_genomic.fna/checkm_result
[2024-01-24 11:15:00,543] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:00,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:00,574] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:00,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:00,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019429605.1_ASM1942960v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:00,575] [INFO] Task started: Blastn
[2024-01-24 11:15:00,575] [INFO] Running command: blastn -query GCF_019429605.1_ASM1942960v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfde59d26-e323-4848-945f-fb3f75bc9a15/dqc_reference/reference_markers_gtdb.fasta -out GCF_019429605.1_ASM1942960v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:02,360] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:02,364] [INFO] Selected 11 target genomes.
[2024-01-24 11:15:02,365] [INFO] Target genome list was writen to GCF_019429605.1_ASM1942960v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:02,373] [INFO] Task started: fastANI
[2024-01-24 11:15:02,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg535a029c-6f03-45e1-96a7-2089bce27149/GCF_019429605.1_ASM1942960v1_genomic.fna.gz --refList GCF_019429605.1_ASM1942960v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019429605.1_ASM1942960v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:31,781] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:31,794] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:15:31,794] [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_014647795.1	s__Actinoplanes campanulatus	96.2918	2722	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	inconclusive
GCF_014205215.1	s__Actinoplanes lobatus	95.0824	2715	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	inconclusive
GCF_017592555.1	s__Actinoplanes sp017592555	94.0407	2565	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862455.1	s__Actinoplanes utahensis	85.1137	1959	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	85.0555	2104	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	84.9868	2091	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900104725.1	s__Actinoplanes derwentensis	84.0293	1905	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014205225.1	s__Actinoplanes octamycinicus	83.0648	1842	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004001265.1	s__Actinoplanes sp004001265	83.0131	1810	3076	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	82.8144	1554	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.8079	1833	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:31,796] [INFO] GTDB search result was written to GCF_019429605.1_ASM1942960v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:31,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:31,800] [INFO] DFAST_QC result json was written to GCF_019429605.1_ASM1942960v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:31,800] [INFO] DFAST_QC completed!
[2024-01-24 11:15:31,800] [INFO] Total running time: 0h2m52s