[2024-01-25 20:11:50,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:50,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:50,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference
[2024-01-25 20:11:51,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:51,879] [INFO] Task started: Prodigal
[2024-01-25 20:11:51,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg016ce7d2-f331-4284-82a4-318c0400bf9f/GCF_016862355.1_ASM1686235v1_genomic.fna.gz | prodigal -d GCF_016862355.1_ASM1686235v1_genomic.fna/cds.fna -a GCF_016862355.1_ASM1686235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:15,796] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:15,796] [INFO] Task started: HMMsearch
[2024-01-25 20:12:15,796] [INFO] Running command: hmmsearch --tblout GCF_016862355.1_ASM1686235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference/reference_markers.hmm GCF_016862355.1_ASM1686235v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:16,137] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:16,141] [INFO] Found 6/6 markers.
[2024-01-25 20:12:16,215] [INFO] Query marker FASTA was written to GCF_016862355.1_ASM1686235v1_genomic.fna/markers.fasta
[2024-01-25 20:12:16,215] [INFO] Task started: Blastn
[2024-01-25 20:12:16,215] [INFO] Running command: blastn -query GCF_016862355.1_ASM1686235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference/reference_markers.fasta -out GCF_016862355.1_ASM1686235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:17,363] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:17,365] [INFO] Selected 13 target genomes.
[2024-01-25 20:12:17,366] [INFO] Target genome list was writen to GCF_016862355.1_ASM1686235v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:17,375] [INFO] Task started: fastANI
[2024-01-25 20:12:17,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg016ce7d2-f331-4284-82a4-318c0400bf9f/GCF_016862355.1_ASM1686235v1_genomic.fna.gz --refList GCF_016862355.1_ASM1686235v1_genomic.fna/target_genomes.txt --output GCF_016862355.1_ASM1686235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:45,453] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:45,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:45,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:45,462] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:12:45,462] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:45,462] [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 regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	100.0	3229	3233	95	conclusive
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	99.9979	3228	3233	95	conclusive
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	85.8297	1741	3233	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	85.7806	2054	3233	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	85.7312	2011	3233	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	85.6943	1807	3233	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	85.6892	1815	3233	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	85.6425	2040	3233	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.6904	1793	3233	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.0208	849	3233	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.9086	1133	3233	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8587	928	3233	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.7702	1066	3233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:45,463] [INFO] DFAST Taxonomy check result was written to GCF_016862355.1_ASM1686235v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:45,464] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:45,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:45,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference/checkm_data
[2024-01-25 20:12:45,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:45,555] [INFO] Task started: CheckM
[2024-01-25 20:12:45,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862355.1_ASM1686235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862355.1_ASM1686235v1_genomic.fna/checkm_input GCF_016862355.1_ASM1686235v1_genomic.fna/checkm_result
[2024-01-25 20:14:10,630] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:10,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:10,655] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:10,656] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:10,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862355.1_ASM1686235v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:10,657] [INFO] Task started: Blastn
[2024-01-25 20:14:10,657] [INFO] Running command: blastn -query GCF_016862355.1_ASM1686235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd77796da-4e02-4b7d-8db4-77c6fa1bfc28/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862355.1_ASM1686235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:12,471] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:12,474] [INFO] Selected 9 target genomes.
[2024-01-25 20:14:12,474] [INFO] Target genome list was writen to GCF_016862355.1_ASM1686235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:12,480] [INFO] Task started: fastANI
[2024-01-25 20:14:12,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg016ce7d2-f331-4284-82a4-318c0400bf9f/GCF_016862355.1_ASM1686235v1_genomic.fna.gz --refList GCF_016862355.1_ASM1686235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862355.1_ASM1686235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:38,358] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:38,364] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:38,365] [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_900188005.1	s__Actinoplanes regularis	99.9979	3228	3233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016862395.1	s__Actinoplanes siamensis	86.1176	1821	3233	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	85.806	2049	3233	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	85.6931	1814	3233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	85.6419	2041	3233	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	85.553	2079	3233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCA_000715855.1	s__Actinoplanes liguriensis	85.4094	2126	3233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	85.2727	2058	3233	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	84.7918	1883	3233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:38,398] [INFO] GTDB search result was written to GCF_016862355.1_ASM1686235v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:38,399] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:38,402] [INFO] DFAST_QC result json was written to GCF_016862355.1_ASM1686235v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:38,402] [INFO] DFAST_QC completed!
[2024-01-25 20:14:38,402] [INFO] Total running time: 0h2m48s