[2024-01-24 12:37:09,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference
[2024-01-24 12:37:10,705] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,706] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,706] [INFO] Running command: gunzip -c /var/lib/cwl/stg804da6bf-f16d-4339-9bcf-0f60c022da5d/GCF_016862235.1_ASM1686223v1_genomic.fna.gz | prodigal -d GCF_016862235.1_ASM1686223v1_genomic.fna/cds.fna -a GCF_016862235.1_ASM1686223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:41,821] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:41,822] [INFO] Task started: HMMsearch
[2024-01-24 12:37:41,822] [INFO] Running command: hmmsearch --tblout GCF_016862235.1_ASM1686223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference/reference_markers.hmm GCF_016862235.1_ASM1686223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:42,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:42,258] [INFO] Found 6/6 markers.
[2024-01-24 12:37:42,340] [INFO] Query marker FASTA was written to GCF_016862235.1_ASM1686223v1_genomic.fna/markers.fasta
[2024-01-24 12:37:42,340] [INFO] Task started: Blastn
[2024-01-24 12:37:42,341] [INFO] Running command: blastn -query GCF_016862235.1_ASM1686223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference/reference_markers.fasta -out GCF_016862235.1_ASM1686223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:43,568] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:43,572] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:43,573] [INFO] Target genome list was writen to GCF_016862235.1_ASM1686223v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:43,580] [INFO] Task started: fastANI
[2024-01-24 12:37:43,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg804da6bf-f16d-4339-9bcf-0f60c022da5d/GCF_016862235.1_ASM1686223v1_genomic.fna.gz --refList GCF_016862235.1_ASM1686223v1_genomic.fna/target_genomes.txt --output GCF_016862235.1_ASM1686223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:25,268] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:25,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:25,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:25,286] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:38:25,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:25,286] [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 italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	100.0	3564	3577	95	conclusive
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	99.9917	3568	3577	95	conclusive
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	86.22	2379	3577	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	86.1954	2359	3577	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	86.1718	2437	3577	95	below_threshold
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	85.0192	2138	3577	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	85.009	2108	3577	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	84.9827	2073	3577	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	84.9702	2149	3577	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.7959	2155	3577	95	below_threshold
Actinoplanes derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	83.7614	2013	3577	95	below_threshold
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	83.7155	2070	3577	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	81.8833	1819	3577	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4361	1409	3577	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.3429	1149	3577	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	76.5012	714	3577	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.0024	727	3577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:25,288] [INFO] DFAST Taxonomy check result was written to GCF_016862235.1_ASM1686223v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:25,288] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:25,288] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:25,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference/checkm_data
[2024-01-24 12:38:25,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:25,392] [INFO] Task started: CheckM
[2024-01-24 12:38:25,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862235.1_ASM1686223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862235.1_ASM1686223v1_genomic.fna/checkm_input GCF_016862235.1_ASM1686223v1_genomic.fna/checkm_result
[2024-01-24 12:40:03,931] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:03,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:03,973] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:03,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:03,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862235.1_ASM1686223v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:03,976] [INFO] Task started: Blastn
[2024-01-24 12:40:03,977] [INFO] Running command: blastn -query GCF_016862235.1_ASM1686223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658dc1a2-0233-472c-a0ac-26297ab6af78/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862235.1_ASM1686223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:05,852] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:05,857] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:05,857] [INFO] Target genome list was writen to GCF_016862235.1_ASM1686223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:05,866] [INFO] Task started: fastANI
[2024-01-24 12:40:05,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg804da6bf-f16d-4339-9bcf-0f60c022da5d/GCF_016862235.1_ASM1686223v1_genomic.fna.gz --refList GCF_016862235.1_ASM1686223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862235.1_ASM1686223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:44,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:44,558] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:44,558] [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_003001815.1	s__Actinoplanes italicus	99.9917	3568	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_900113015.1	s__Actinoplanes philippinensis	86.213	2381	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	86.1897	2433	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647795.1	s__Actinoplanes campanulatus	84.9776	2146	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_016862455.1	s__Actinoplanes utahensis	84.9628	2076	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862075.1	s__Actinoplanes couchii	83.7621	2134	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104725.1	s__Actinoplanes derwentensis	83.7506	2063	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015704865.1	s__Actinoplanes sp015704865	82.9403	2034	3577	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	82.9058	1885	3577	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	82.6654	1886	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	82.2863	1703	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862095.1	s__Actinoplanes cyaneus	81.8725	1821	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	81.7393	1677	3577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003999975.1	s__Actinoplanes sp003999975	80.1717	1610	3577	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 12:40:44,560] [INFO] GTDB search result was written to GCF_016862235.1_ASM1686223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:44,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:44,566] [INFO] DFAST_QC result json was written to GCF_016862235.1_ASM1686223v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:44,566] [INFO] DFAST_QC completed!
[2024-01-24 12:40:44,567] [INFO] Total running time: 0h3m35s