[2024-01-25 19:09:20,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference
[2024-01-25 19:09:21,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,754] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bb6c524-e42b-48ba-9921-d45bdb90b971/GCF_016862415.1_ASM1686241v1_genomic.fna.gz | prodigal -d GCF_016862415.1_ASM1686241v1_genomic.fna/cds.fna -a GCF_016862415.1_ASM1686241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:40,866] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:40,866] [INFO] Task started: HMMsearch
[2024-01-25 19:09:40,866] [INFO] Running command: hmmsearch --tblout GCF_016862415.1_ASM1686241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference/reference_markers.hmm GCF_016862415.1_ASM1686241v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:41,164] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:41,165] [INFO] Found 6/6 markers.
[2024-01-25 19:09:41,230] [INFO] Query marker FASTA was written to GCF_016862415.1_ASM1686241v1_genomic.fna/markers.fasta
[2024-01-25 19:09:41,230] [INFO] Task started: Blastn
[2024-01-25 19:09:41,230] [INFO] Running command: blastn -query GCF_016862415.1_ASM1686241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference/reference_markers.fasta -out GCF_016862415.1_ASM1686241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:42,426] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:42,429] [INFO] Selected 14 target genomes.
[2024-01-25 19:09:42,429] [INFO] Target genome list was writen to GCF_016862415.1_ASM1686241v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:42,441] [INFO] Task started: fastANI
[2024-01-25 19:09:42,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb6c524-e42b-48ba-9921-d45bdb90b971/GCF_016862415.1_ASM1686241v1_genomic.fna.gz --refList GCF_016862415.1_ASM1686241v1_genomic.fna/target_genomes.txt --output GCF_016862415.1_ASM1686241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:13,967] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:13,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:13,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:13,978] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:10:13,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:13,978] [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 teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	100.0	2608	2624	95	conclusive
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	99.9968	2623	2624	95	conclusive
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	99.994	2609	2624	95	conclusive
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	86.3959	1871	2624	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	86.3247	1912	2624	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	86.1074	1856	2624	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	86.01	1851	2624	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	85.8138	1770	2624	95	below_threshold
Actinoplanes regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	85.783	1738	2624	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.9789	1614	2624	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.6107	834	2624	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.4148	1139	2624	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.2983	973	2624	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	79.1258	1141	2624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:13,980] [INFO] DFAST Taxonomy check result was written to GCF_016862415.1_ASM1686241v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:13,980] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:13,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:13,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference/checkm_data
[2024-01-25 19:10:13,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:14,058] [INFO] Task started: CheckM
[2024-01-25 19:10:14,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862415.1_ASM1686241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862415.1_ASM1686241v1_genomic.fna/checkm_input GCF_016862415.1_ASM1686241v1_genomic.fna/checkm_result
[2024-01-25 19:11:41,525] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:41,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:41,548] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:41,548] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:41,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862415.1_ASM1686241v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:41,549] [INFO] Task started: Blastn
[2024-01-25 19:11:41,549] [INFO] Running command: blastn -query GCF_016862415.1_ASM1686241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97e8b59b-69b0-410e-9878-e28fbcd4ad61/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862415.1_ASM1686241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:43,453] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:43,457] [INFO] Selected 9 target genomes.
[2024-01-25 19:11:43,457] [INFO] Target genome list was writen to GCF_016862415.1_ASM1686241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:43,466] [INFO] Task started: fastANI
[2024-01-25 19:11:43,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb6c524-e42b-48ba-9921-d45bdb90b971/GCF_016862415.1_ASM1686241v1_genomic.fna.gz --refList GCF_016862415.1_ASM1686241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862415.1_ASM1686241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:08,129] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:08,135] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:08,135] [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_003711105.1	s__Actinoplanes teichomyceticus	99.9968	2623	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	conclusive
GCF_014205225.1	s__Actinoplanes octamycinicus	86.3143	1913	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862395.1	s__Actinoplanes siamensis	86.249	1761	2624	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	86.0589	1909	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	86.0257	1847	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900188005.1	s__Actinoplanes regularis	85.8001	1772	2624	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	85.1291	1724	2624	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	84.975	1848	2624	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	83.1932	1648	2624	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 19:12:08,137] [INFO] GTDB search result was written to GCF_016862415.1_ASM1686241v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:08,137] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:08,140] [INFO] DFAST_QC result json was written to GCF_016862415.1_ASM1686241v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:08,141] [INFO] DFAST_QC completed!
[2024-01-25 19:12:08,141] [INFO] Total running time: 0h2m48s