[2024-01-24 13:28:25,837] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference
[2024-01-24 13:28:27,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,236] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,236] [INFO] Running command: gunzip -c /var/lib/cwl/stgd12e26be-450d-4838-9977-a513121f7daa/GCF_031454295.1_ASM3145429v1_genomic.fna.gz | prodigal -d GCF_031454295.1_ASM3145429v1_genomic.fna/cds.fna -a GCF_031454295.1_ASM3145429v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:09,972] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:09,973] [INFO] Task started: HMMsearch
[2024-01-24 13:29:09,973] [INFO] Running command: hmmsearch --tblout GCF_031454295.1_ASM3145429v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference/reference_markers.hmm GCF_031454295.1_ASM3145429v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:10,529] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:10,531] [INFO] Found 6/6 markers.
[2024-01-24 13:29:10,619] [INFO] Query marker FASTA was written to GCF_031454295.1_ASM3145429v1_genomic.fna/markers.fasta
[2024-01-24 13:29:10,620] [INFO] Task started: Blastn
[2024-01-24 13:29:10,620] [INFO] Running command: blastn -query GCF_031454295.1_ASM3145429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference/reference_markers.fasta -out GCF_031454295.1_ASM3145429v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:11,833] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:11,837] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:11,838] [INFO] Target genome list was writen to GCF_031454295.1_ASM3145429v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:11,860] [INFO] Task started: fastANI
[2024-01-24 13:29:11,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgd12e26be-450d-4838-9977-a513121f7daa/GCF_031454295.1_ASM3145429v1_genomic.fna.gz --refList GCF_031454295.1_ASM3145429v1_genomic.fna/target_genomes.txt --output GCF_031454295.1_ASM3145429v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:52,788] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:52,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:52,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:52,803] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:29:52,803] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:29:52,803] [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 derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	87.8076	2522	3873	95	below_threshold
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	87.7342	2576	3873	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	84.401	2009	3873	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	84.2695	2226	3873	95	below_threshold
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	84.226	2236	3873	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	84.0378	2183	3873	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	83.9162	2043	3873	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	83.9115	2016	3873	95	below_threshold
Actinoplanes lobatus	strain=DSM 43150	GCA_014205215.1	113568	113568	type	True	83.8308	2126	3873	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	83.8163	2097	3873	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	83.7458	2190	3873	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	83.6831	2216	3873	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.5657	976	3873	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.3294	933	3873	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.2608	1398	3873	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.1929	1131	3873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:52,806] [INFO] DFAST Taxonomy check result was written to GCF_031454295.1_ASM3145429v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:52,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:52,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:52,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference/checkm_data
[2024-01-24 13:29:52,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:52,919] [INFO] Task started: CheckM
[2024-01-24 13:29:52,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031454295.1_ASM3145429v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031454295.1_ASM3145429v1_genomic.fna/checkm_input GCF_031454295.1_ASM3145429v1_genomic.fna/checkm_result
[2024-01-24 13:32:27,924] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:27,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:27,956] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:27,956] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:27,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031454295.1_ASM3145429v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:27,957] [INFO] Task started: Blastn
[2024-01-24 13:32:27,957] [INFO] Running command: blastn -query GCF_031454295.1_ASM3145429v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe96d460-7f67-42ac-9d68-4ea4809dfcc9/dqc_reference/reference_markers_gtdb.fasta -out GCF_031454295.1_ASM3145429v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:29,800] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:29,807] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:29,807] [INFO] Target genome list was writen to GCF_031454295.1_ASM3145429v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:29,830] [INFO] Task started: fastANI
[2024-01-24 13:32:29,830] [INFO] Running command: fastANI --query /var/lib/cwl/stgd12e26be-450d-4838-9977-a513121f7daa/GCF_031454295.1_ASM3145429v1_genomic.fna.gz --refList GCF_031454295.1_ASM3145429v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031454295.1_ASM3145429v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:02,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,970] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:02,971] [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_016862075.1	s__Actinoplanes couchii	99.9488	3714	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104725.1	s__Actinoplanes derwentensis	87.7418	2572	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862455.1	s__Actinoplanes utahensis	84.428	2003	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	84.2307	2233	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	84.0242	2186	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017592555.1	s__Actinoplanes sp017592555	83.9186	2015	3873	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	83.8295	2127	3873	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	83.816	2097	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_003001815.1	s__Actinoplanes italicus	83.6124	2234	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	81.9843	1844	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003751945.1	s__Actinoplanes caeruleus	79.7172	1279	3873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,977] [INFO] GTDB search result was written to GCF_031454295.1_ASM3145429v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:02,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:02,981] [INFO] DFAST_QC result json was written to GCF_031454295.1_ASM3145429v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:02,982] [INFO] DFAST_QC completed!
[2024-01-24 13:33:02,982] [INFO] Total running time: 0h4m37s