[2024-01-25 20:20:05,880] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:05,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:05,881] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference
[2024-01-25 20:20:07,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:07,113] [INFO] Task started: Prodigal
[2024-01-25 20:20:07,113] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3a18916-3cad-4cc3-92c2-0fef464c944b/GCF_000763095.1_ASM76309v1_genomic.fna.gz | prodigal -d GCF_000763095.1_ASM76309v1_genomic.fna/cds.fna -a GCF_000763095.1_ASM76309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:21,554] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:21,554] [INFO] Task started: HMMsearch
[2024-01-25 20:20:21,554] [INFO] Running command: hmmsearch --tblout GCF_000763095.1_ASM76309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference/reference_markers.hmm GCF_000763095.1_ASM76309v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:21,898] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:21,899] [INFO] Found 6/6 markers.
[2024-01-25 20:20:21,942] [INFO] Query marker FASTA was written to GCF_000763095.1_ASM76309v1_genomic.fna/markers.fasta
[2024-01-25 20:20:21,943] [INFO] Task started: Blastn
[2024-01-25 20:20:21,943] [INFO] Running command: blastn -query GCF_000763095.1_ASM76309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference/reference_markers.fasta -out GCF_000763095.1_ASM76309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:23,127] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:23,130] [INFO] Selected 12 target genomes.
[2024-01-25 20:20:23,130] [INFO] Target genome list was writen to GCF_000763095.1_ASM76309v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:23,156] [INFO] Task started: fastANI
[2024-01-25 20:20:23,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a18916-3cad-4cc3-92c2-0fef464c944b/GCF_000763095.1_ASM76309v1_genomic.fna.gz --refList GCF_000763095.1_ASM76309v1_genomic.fna/target_genomes.txt --output GCF_000763095.1_ASM76309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:37,983] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:37,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:37,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:37,992] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:20:37,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:37,992] [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
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	100.0	1771	1771	95	conclusive
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	99.981	1730	1771	95	conclusive
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	94.4877	1460	1771	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	86.9962	1367	1771	95	below_threshold
Actinopolyspora alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	86.9371	1380	1771	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	82.0506	1046	1771	95	below_threshold
Actinopolyspora halophila	strain=DSM 43834	GCA_000371785.1	1850	1850	type	True	81.8678	1030	1771	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000062885.1	1836	1836	type	True	79.3567	737	1771	95	below_threshold
Saccharopolyspora erythraea	strain=NRRL 2338	GCA_000171635.1	1836	1836	type	True	79.3027	716	1771	95	below_threshold
Saccharopolyspora erythraea	strain=DSM 40517	GCA_002564065.1	1836	1836	type	True	79.2908	748	1771	95	below_threshold
Saccharopolyspora rectivirgula	strain=DSM 43747	GCA_000497205.1	28042	28042	type	True	78.7372	512	1771	95	below_threshold
Amycolatopsis panacis	strain=YIM PH21725	GCA_003600245.1	2340917	2340917	type	True	77.2055	335	1771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:38,003] [INFO] DFAST Taxonomy check result was written to GCF_000763095.1_ASM76309v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:38,005] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:38,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:38,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference/checkm_data
[2024-01-25 20:20:38,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:38,060] [INFO] Task started: CheckM
[2024-01-25 20:20:38,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000763095.1_ASM76309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000763095.1_ASM76309v1_genomic.fna/checkm_input GCF_000763095.1_ASM76309v1_genomic.fna/checkm_result
[2024-01-25 20:21:27,453] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:27,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:27,475] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:27,475] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:27,475] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000763095.1_ASM76309v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:27,476] [INFO] Task started: Blastn
[2024-01-25 20:21:27,476] [INFO] Running command: blastn -query GCF_000763095.1_ASM76309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f71341-2d79-4293-8161-1bbb50bde4c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000763095.1_ASM76309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:29,242] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:29,249] [INFO] Selected 8 target genomes.
[2024-01-25 20:21:29,249] [INFO] Target genome list was writen to GCF_000763095.1_ASM76309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:29,258] [INFO] Task started: fastANI
[2024-01-25 20:21:29,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a18916-3cad-4cc3-92c2-0fef464c944b/GCF_000763095.1_ASM76309v1_genomic.fna.gz --refList GCF_000763095.1_ASM76309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000763095.1_ASM76309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:39,867] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:39,873] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:39,873] [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_002263515.1	s__Actinopolyspora erythraea	99.981	1730	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_900104475.1	s__Actinopolyspora xinjiangensis	94.4887	1460	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116555.1	s__Actinopolyspora righensis	87.0076	1366	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
GCF_900112765.1	s__Actinopolyspora alba	86.9493	1378	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	N/A	N/A	N/A	N/A	1	-
GCF_900101095.1	s__Actinopolyspora mzabensis	86.4292	1322	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100925.1	s__Actinopolyspora saharensis	82.2087	1027	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_013408175.1	s__Actinopolyspora biskrensis	82.051	1046	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716775.1	s__Actinopolyspora sp006716775	81.9768	1004	1771	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:39,875] [INFO] GTDB search result was written to GCF_000763095.1_ASM76309v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:39,875] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:39,878] [INFO] DFAST_QC result json was written to GCF_000763095.1_ASM76309v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:39,878] [INFO] DFAST_QC completed!
[2024-01-25 20:21:39,878] [INFO] Total running time: 0h1m34s