[2024-01-24 13:23:11,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:11,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:11,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference
[2024-01-24 13:23:12,671] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,672] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,673] [INFO] Running command: gunzip -c /var/lib/cwl/stg802acee2-bc76-42ea-92bc-2f89946b9cb4/GCF_025960925.1_ASM2596092v1_genomic.fna.gz | prodigal -d GCF_025960925.1_ASM2596092v1_genomic.fna/cds.fna -a GCF_025960925.1_ASM2596092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:43,211] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:43,212] [INFO] Task started: HMMsearch
[2024-01-24 13:23:43,212] [INFO] Running command: hmmsearch --tblout GCF_025960925.1_ASM2596092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference/reference_markers.hmm GCF_025960925.1_ASM2596092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:43,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:43,638] [INFO] Found 6/6 markers.
[2024-01-24 13:23:43,720] [INFO] Query marker FASTA was written to GCF_025960925.1_ASM2596092v1_genomic.fna/markers.fasta
[2024-01-24 13:23:43,721] [INFO] Task started: Blastn
[2024-01-24 13:23:43,721] [INFO] Running command: blastn -query GCF_025960925.1_ASM2596092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference/reference_markers.fasta -out GCF_025960925.1_ASM2596092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:44,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:44,976] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:44,977] [INFO] Target genome list was writen to GCF_025960925.1_ASM2596092v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:44,999] [INFO] Task started: fastANI
[2024-01-24 13:23:44,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg802acee2-bc76-42ea-92bc-2f89946b9cb4/GCF_025960925.1_ASM2596092v1_genomic.fna.gz --refList GCF_025960925.1_ASM2596092v1_genomic.fna/target_genomes.txt --output GCF_025960925.1_ASM2596092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:24:19,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:19,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:24:19,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:24:19,604] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:24:19,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:24:19,604] [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 cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	99.979	3340	3429	95	conclusive
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	85.3525	2186	3429	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	85.3431	2212	3429	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	85.3104	2250	3429	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	85.2508	2172	3429	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	85.1066	2138	3429	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	84.8735	1901	3429	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	84.8438	1952	3429	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	84.8143	1964	3429	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.0279	1802	3429	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.8612	851	3429	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.7087	997	3429	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.6723	1190	3429	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.3905	1170	3429	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:24:19,606] [INFO] DFAST Taxonomy check result was written to GCF_025960925.1_ASM2596092v1_genomic.fna/tc_result.tsv
[2024-01-24 13:24:19,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:24:19,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:24:19,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference/checkm_data
[2024-01-24 13:24:19,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:24:19,700] [INFO] Task started: CheckM
[2024-01-24 13:24:19,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025960925.1_ASM2596092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025960925.1_ASM2596092v1_genomic.fna/checkm_input GCF_025960925.1_ASM2596092v1_genomic.fna/checkm_result
[2024-01-24 13:26:05,301] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:05,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:05,332] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:05,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:05,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025960925.1_ASM2596092v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:05,333] [INFO] Task started: Blastn
[2024-01-24 13:26:05,334] [INFO] Running command: blastn -query GCF_025960925.1_ASM2596092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2854b79d-28ad-4bb1-8992-31b39e2939d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_025960925.1_ASM2596092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:07,254] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:07,259] [INFO] Selected 9 target genomes.
[2024-01-24 13:26:07,259] [INFO] Target genome list was writen to GCF_025960925.1_ASM2596092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:07,308] [INFO] Task started: fastANI
[2024-01-24 13:26:07,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg802acee2-bc76-42ea-92bc-2f89946b9cb4/GCF_025960925.1_ASM2596092v1_genomic.fna.gz --refList GCF_025960925.1_ASM2596092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025960925.1_ASM2596092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:34,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:34,908] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:34,908] [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_016862095.1	s__Actinoplanes cyaneus	99.979	3340	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000715855.1	s__Actinoplanes liguriensis	88.6713	2540	3429	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	86.0356	2017	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	85.3915	2178	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014205225.1	s__Actinoplanes octamycinicus	85.3112	2249	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188005.1	s__Actinoplanes regularis	85.1106	2139	3429	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	84.811	1964	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_900119315.1	s__Actinoplanes sp900119315	84.7745	2049	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016862455.1	s__Actinoplanes utahensis	82.3038	1784	3429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:34,910] [INFO] GTDB search result was written to GCF_025960925.1_ASM2596092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:34,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:34,914] [INFO] DFAST_QC result json was written to GCF_025960925.1_ASM2596092v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:34,914] [INFO] DFAST_QC completed!
[2024-01-24 13:26:34,914] [INFO] Total running time: 0h3m24s