[2024-01-24 11:58:55,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference
[2024-01-24 11:58:57,089] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,091] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgd75973ce-82f3-4dd6-9edc-ae58694c24d5/GCF_018324205.1_ASM1832420v1_genomic.fna.gz | prodigal -d GCF_018324205.1_ASM1832420v1_genomic.fna/cds.fna -a GCF_018324205.1_ASM1832420v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:25,090] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:25,090] [INFO] Task started: HMMsearch
[2024-01-24 11:59:25,090] [INFO] Running command: hmmsearch --tblout GCF_018324205.1_ASM1832420v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference/reference_markers.hmm GCF_018324205.1_ASM1832420v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:25,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:25,550] [INFO] Found 6/6 markers.
[2024-01-24 11:59:25,625] [INFO] Query marker FASTA was written to GCF_018324205.1_ASM1832420v1_genomic.fna/markers.fasta
[2024-01-24 11:59:25,626] [INFO] Task started: Blastn
[2024-01-24 11:59:25,626] [INFO] Running command: blastn -query GCF_018324205.1_ASM1832420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference/reference_markers.fasta -out GCF_018324205.1_ASM1832420v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:26,913] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:26,917] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:26,917] [INFO] Target genome list was writen to GCF_018324205.1_ASM1832420v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:26,922] [INFO] Task started: fastANI
[2024-01-24 11:59:26,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75973ce-82f3-4dd6-9edc-ae58694c24d5/GCF_018324205.1_ASM1832420v1_genomic.fna.gz --refList GCF_018324205.1_ASM1832420v1_genomic.fna/target_genomes.txt --output GCF_018324205.1_ASM1832420v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:03,273] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:03,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:03,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:03,285] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:00:03,285] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:03,285] [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 ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	100.0	3299	3299	95	conclusive
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	99.9864	3261	3299	95	conclusive
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	90.0888	2568	3299	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	90.0795	2646	3299	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	86.1542	1834	3299	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	86.0835	1943	3299	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	85.4318	2146	3299	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.7848	1828	3299	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	82.719	1850	3299	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.3445	881	3299	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.0835	1239	3299	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8749	1032	3299	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.7488	1180	3299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:03,287] [INFO] DFAST Taxonomy check result was written to GCF_018324205.1_ASM1832420v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:03,287] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:03,287] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:03,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference/checkm_data
[2024-01-24 12:00:03,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:03,376] [INFO] Task started: CheckM
[2024-01-24 12:00:03,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018324205.1_ASM1832420v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018324205.1_ASM1832420v1_genomic.fna/checkm_input GCF_018324205.1_ASM1832420v1_genomic.fna/checkm_result
[2024-01-24 12:01:56,130] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:56,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:56,158] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:56,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:56,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018324205.1_ASM1832420v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:56,158] [INFO] Task started: Blastn
[2024-01-24 12:01:56,159] [INFO] Running command: blastn -query GCF_018324205.1_ASM1832420v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b267a03-95cc-49c8-9744-84d2b94ae3f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_018324205.1_ASM1832420v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:57,952] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:57,957] [INFO] Selected 12 target genomes.
[2024-01-24 12:01:57,957] [INFO] Target genome list was writen to GCF_018324205.1_ASM1832420v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:57,964] [INFO] Task started: fastANI
[2024-01-24 12:01:57,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75973ce-82f3-4dd6-9edc-ae58694c24d5/GCF_018324205.1_ASM1832420v1_genomic.fna.gz --refList GCF_018324205.1_ASM1832420v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018324205.1_ASM1832420v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:32,331] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:32,342] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:32,342] [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_018324205.1	s__Actinoplanes ianthinogenes	100.0	3299	3299	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_014205225.1	s__Actinoplanes octamycinicus	90.1114	2641	3299	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	86.0447	1946	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862395.1	s__Actinoplanes siamensis	86.01	1878	3299	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	85.7854	2262	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_900188005.1	s__Actinoplanes regularis	85.6258	2077	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900119315.1	s__Actinoplanes sp900119315	85.5256	2071	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016862095.1	s__Actinoplanes cyaneus	85.414	2148	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715855.1	s__Actinoplanes liguriensis	85.378	2252	3299	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	82.858	1932	3299	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	82.7445	1902	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_014647795.1	s__Actinoplanes campanulatus	82.7128	1831	3299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:32,343] [INFO] GTDB search result was written to GCF_018324205.1_ASM1832420v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:32,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:32,347] [INFO] DFAST_QC result json was written to GCF_018324205.1_ASM1832420v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:32,347] [INFO] DFAST_QC completed!
[2024-01-24 12:02:32,347] [INFO] Total running time: 0h3m37s