[2024-01-25 20:27:50,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:50,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:50,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference
[2024-01-25 20:27:51,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:51,721] [INFO] Task started: Prodigal
[2024-01-25 20:27:51,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b3040a1-9647-44eb-a831-d6bcbc1393da/GCF_020216025.1_ASM2021602v1_genomic.fna.gz | prodigal -d GCF_020216025.1_ASM2021602v1_genomic.fna/cds.fna -a GCF_020216025.1_ASM2021602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:28:20,785] [INFO] Task succeeded: Prodigal
[2024-01-25 20:28:20,786] [INFO] Task started: HMMsearch
[2024-01-25 20:28:20,786] [INFO] Running command: hmmsearch --tblout GCF_020216025.1_ASM2021602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference/reference_markers.hmm GCF_020216025.1_ASM2021602v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:28:21,191] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:28:21,192] [INFO] Found 6/6 markers.
[2024-01-25 20:28:21,266] [INFO] Query marker FASTA was written to GCF_020216025.1_ASM2021602v1_genomic.fna/markers.fasta
[2024-01-25 20:28:21,266] [INFO] Task started: Blastn
[2024-01-25 20:28:21,267] [INFO] Running command: blastn -query GCF_020216025.1_ASM2021602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference/reference_markers.fasta -out GCF_020216025.1_ASM2021602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:22,478] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:22,481] [INFO] Selected 23 target genomes.
[2024-01-25 20:28:22,482] [INFO] Target genome list was writen to GCF_020216025.1_ASM2021602v1_genomic.fna/target_genomes.txt
[2024-01-25 20:28:22,496] [INFO] Task started: fastANI
[2024-01-25 20:28:22,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b3040a1-9647-44eb-a831-d6bcbc1393da/GCF_020216025.1_ASM2021602v1_genomic.fna.gz --refList GCF_020216025.1_ASM2021602v1_genomic.fna/target_genomes.txt --output GCF_020216025.1_ASM2021602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:29:14,698] [INFO] Task succeeded: fastANI
[2024-01-25 20:29:14,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:29:14,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:29:14,711] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:29:14,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:29:14,712] [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 auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	81.9624	1789	3196	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	81.9451	1745	3196	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	81.5492	1663	3196	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	81.544	1625	3196	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	81.1657	1296	3196	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	81.0368	1432	3196	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	81.0276	1660	3196	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	80.9283	1462	3196	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	80.92	1469	3196	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	80.91	1418	3196	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	80.8728	1632	3196	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	80.6451	1599	3196	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	80.6233	1639	3196	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	80.4904	1545	3196	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.3747	1496	3196	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	80.2191	1619	3196	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	80.2135	1556	3196	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	80.1823	1469	3196	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	80.0215	1571	3196	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.5975	877	3196	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.3165	1036	3196	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.5881	1440	3196	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.492	1000	3196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:29:14,713] [INFO] DFAST Taxonomy check result was written to GCF_020216025.1_ASM2021602v1_genomic.fna/tc_result.tsv
[2024-01-25 20:29:14,713] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:29:14,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:29:14,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference/checkm_data
[2024-01-25 20:29:14,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:29:14,803] [INFO] Task started: CheckM
[2024-01-25 20:29:14,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020216025.1_ASM2021602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020216025.1_ASM2021602v1_genomic.fna/checkm_input GCF_020216025.1_ASM2021602v1_genomic.fna/checkm_result
[2024-01-25 20:31:29,391] [INFO] Task succeeded: CheckM
[2024-01-25 20:31:29,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:31:29,414] [INFO] ===== Completeness check finished =====
[2024-01-25 20:31:29,415] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:31:29,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020216025.1_ASM2021602v1_genomic.fna/markers.fasta)
[2024-01-25 20:31:29,416] [INFO] Task started: Blastn
[2024-01-25 20:31:29,416] [INFO] Running command: blastn -query GCF_020216025.1_ASM2021602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fab7c74-46c5-4a68-97c8-91f0307e2da6/dqc_reference/reference_markers_gtdb.fasta -out GCF_020216025.1_ASM2021602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:31:31,240] [INFO] Task succeeded: Blastn
[2024-01-25 20:31:31,245] [INFO] Selected 19 target genomes.
[2024-01-25 20:31:31,245] [INFO] Target genome list was writen to GCF_020216025.1_ASM2021602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:31:31,373] [INFO] Task started: fastANI
[2024-01-25 20:31:31,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b3040a1-9647-44eb-a831-d6bcbc1393da/GCF_020216025.1_ASM2021602v1_genomic.fna.gz --refList GCF_020216025.1_ASM2021602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020216025.1_ASM2021602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:32:16,536] [INFO] Task succeeded: fastANI
[2024-01-25 20:32:16,548] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:32:16,548] [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_016862275.1	s__Actinoplanes nipponensis	82.006	1729	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332655.1	s__Actinoplanes auranticolor	81.9534	1792	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	81.6908	1635	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014205335.1	s__Actinoplanes digitatis	81.62	1650	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	81.5517	1686	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648355.1	s__Actinoplanes azureus	81.3021	1433	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	81.1611	1376	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	81.0206	1435	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000389965.1	s__Actinoplanes sp000389965	80.9458	1525	3196	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	80.9396	1462	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_000494755.1	s__Actinoplanes friuliensis	80.9308	1618	3196	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	80.7893	1362	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646155.1	s__Actinoplanes endophyticus	80.6801	1325	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	80.6553	1629	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	80.4921	1545	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862315.1	s__Actinoplanes palleronii	80.3737	1585	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_018829635.1	s__Actinoplanes bogorensis	80.2285	1551	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000962825.1	s__Actinoplanes rectilineatus	80.0408	1456	3196	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	80.0313	1390	3196	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:32:16,550] [INFO] GTDB search result was written to GCF_020216025.1_ASM2021602v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:32:16,551] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:32:16,555] [INFO] DFAST_QC result json was written to GCF_020216025.1_ASM2021602v1_genomic.fna/dqc_result.json
[2024-01-25 20:32:16,555] [INFO] DFAST_QC completed!
[2024-01-25 20:32:16,555] [INFO] Total running time: 0h4m26s