[2024-01-24 11:51:21,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:21,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:21,221] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference
[2024-01-24 11:51:22,455] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:22,456] [INFO] Task started: Prodigal
[2024-01-24 11:51:22,457] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb8a1cb7-4a6e-4a59-873e-c3ed31c193f5/GCF_018332655.1_ASM1833265v1_genomic.fna.gz | prodigal -d GCF_018332655.1_ASM1833265v1_genomic.fna/cds.fna -a GCF_018332655.1_ASM1833265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:51,475] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:51,475] [INFO] Task started: HMMsearch
[2024-01-24 11:51:51,476] [INFO] Running command: hmmsearch --tblout GCF_018332655.1_ASM1833265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference/reference_markers.hmm GCF_018332655.1_ASM1833265v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:51,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:51,875] [INFO] Found 6/6 markers.
[2024-01-24 11:51:51,955] [INFO] Query marker FASTA was written to GCF_018332655.1_ASM1833265v1_genomic.fna/markers.fasta
[2024-01-24 11:51:51,955] [INFO] Task started: Blastn
[2024-01-24 11:51:51,956] [INFO] Running command: blastn -query GCF_018332655.1_ASM1833265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference/reference_markers.fasta -out GCF_018332655.1_ASM1833265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:53,217] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:53,221] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:53,221] [INFO] Target genome list was writen to GCF_018332655.1_ASM1833265v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:53,253] [INFO] Task started: fastANI
[2024-01-24 11:51:53,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb8a1cb7-4a6e-4a59-873e-c3ed31c193f5/GCF_018332655.1_ASM1833265v1_genomic.fna.gz --refList GCF_018332655.1_ASM1833265v1_genomic.fna/target_genomes.txt --output GCF_018332655.1_ASM1833265v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:15,812] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:15,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:15,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:15,825] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:15,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:15,826] [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 auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	100.0	3226	3231	95	conclusive
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	88.4723	2122	3231	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	84.9634	1839	3231	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	84.9571	1809	3231	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	84.5875	2046	3231	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.3231	1530	3231	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.6063	923	3231	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.3595	1053	3231	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.2395	1221	3231	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	79.145	1222	3231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,828] [INFO] DFAST Taxonomy check result was written to GCF_018332655.1_ASM1833265v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:15,828] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:15,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:15,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference/checkm_data
[2024-01-24 11:52:15,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:15,926] [INFO] Task started: CheckM
[2024-01-24 11:52:15,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018332655.1_ASM1833265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018332655.1_ASM1833265v1_genomic.fna/checkm_input GCF_018332655.1_ASM1833265v1_genomic.fna/checkm_result
[2024-01-24 11:53:51,909] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:51,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:51,943] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:51,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:51,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018332655.1_ASM1833265v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:51,945] [INFO] Task started: Blastn
[2024-01-24 11:53:51,945] [INFO] Running command: blastn -query GCF_018332655.1_ASM1833265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbbab615-dfe0-4729-abeb-f6359d1372fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018332655.1_ASM1833265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:53,819] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:53,824] [INFO] Selected 9 target genomes.
[2024-01-24 11:53:53,824] [INFO] Target genome list was writen to GCF_018332655.1_ASM1833265v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:53,832] [INFO] Task started: fastANI
[2024-01-24 11:53:53,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb8a1cb7-4a6e-4a59-873e-c3ed31c193f5/GCF_018332655.1_ASM1833265v1_genomic.fna.gz --refList GCF_018332655.1_ASM1833265v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018332655.1_ASM1833265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:15,677] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:15,690] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:15,691] [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_018332655.1	s__Actinoplanes auranticolor	100.0	3226	3231	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_016862275.1	s__Actinoplanes nipponensis	88.4477	2126	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	84.9837	1836	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000494755.1	s__Actinoplanes friuliensis	84.5991	2043	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	83.3257	1779	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	83.0836	1839	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	82.5903	1543	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	81.2004	1343	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	80.6707	1624	3231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:15,692] [INFO] GTDB search result was written to GCF_018332655.1_ASM1833265v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:15,693] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:15,696] [INFO] DFAST_QC result json was written to GCF_018332655.1_ASM1833265v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:15,696] [INFO] DFAST_QC completed!
[2024-01-24 11:54:15,696] [INFO] Total running time: 0h2m54s