[2024-01-25 18:03:20,401] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:20,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:20,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference
[2024-01-25 18:03:21,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:21,602] [INFO] Task started: Prodigal
[2024-01-25 18:03:21,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b87eb61-c237-4dc0-bd43-7141b467495e/GCF_016862555.1_ASM1686255v1_genomic.fna.gz | prodigal -d GCF_016862555.1_ASM1686255v1_genomic.fna/cds.fna -a GCF_016862555.1_ASM1686255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:42,515] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:42,516] [INFO] Task started: HMMsearch
[2024-01-25 18:03:42,516] [INFO] Running command: hmmsearch --tblout GCF_016862555.1_ASM1686255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference/reference_markers.hmm GCF_016862555.1_ASM1686255v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:42,832] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:42,833] [INFO] Found 6/6 markers.
[2024-01-25 18:03:42,897] [INFO] Query marker FASTA was written to GCF_016862555.1_ASM1686255v1_genomic.fna/markers.fasta
[2024-01-25 18:03:42,897] [INFO] Task started: Blastn
[2024-01-25 18:03:42,897] [INFO] Running command: blastn -query GCF_016862555.1_ASM1686255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference/reference_markers.fasta -out GCF_016862555.1_ASM1686255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:44,148] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:44,151] [INFO] Selected 9 target genomes.
[2024-01-25 18:03:44,151] [INFO] Target genome list was writen to GCF_016862555.1_ASM1686255v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:44,155] [INFO] Task started: fastANI
[2024-01-25 18:03:44,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b87eb61-c237-4dc0-bd43-7141b467495e/GCF_016862555.1_ASM1686255v1_genomic.fna.gz --refList GCF_016862555.1_ASM1686255v1_genomic.fna/target_genomes.txt --output GCF_016862555.1_ASM1686255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:04,366] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:04,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:04,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:04,377] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:04,377] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:04,377] [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
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	100.0	2813	2823	95	conclusive
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	87.6297	1966	2823	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	86.8696	2080	2823	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	86.4321	2048	2823	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	86.3583	2069	2823	95	below_threshold
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	85.7315	1903	2823	95	below_threshold
Asanoa ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	85.6525	1969	2823	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	79.58	1112	2823	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	79.5053	1039	2823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:04,379] [INFO] DFAST Taxonomy check result was written to GCF_016862555.1_ASM1686255v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:04,379] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:04,379] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:04,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference/checkm_data
[2024-01-25 18:04:04,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:04,461] [INFO] Task started: CheckM
[2024-01-25 18:04:04,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862555.1_ASM1686255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862555.1_ASM1686255v1_genomic.fna/checkm_input GCF_016862555.1_ASM1686255v1_genomic.fna/checkm_result
[2024-01-25 18:05:16,634] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:16,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:16,657] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:16,657] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:16,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862555.1_ASM1686255v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:16,658] [INFO] Task started: Blastn
[2024-01-25 18:05:16,658] [INFO] Running command: blastn -query GCF_016862555.1_ASM1686255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2483582f-f024-4055-b6c3-a4d89f162eeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862555.1_ASM1686255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:18,612] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:18,615] [INFO] Selected 8 target genomes.
[2024-01-25 18:05:18,615] [INFO] Target genome list was writen to GCF_016862555.1_ASM1686255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:18,626] [INFO] Task started: fastANI
[2024-01-25 18:05:18,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b87eb61-c237-4dc0-bd43-7141b467495e/GCF_016862555.1_ASM1686255v1_genomic.fna.gz --refList GCF_016862555.1_ASM1686255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862555.1_ASM1686255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:36,802] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:36,810] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:36,810] [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_016862555.1	s__Asanoa siamensis	100.0	2813	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862515.1	s__Asanoa iriomotensis	87.6249	1966	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188485.1	s__Asanoa hainanensis	86.8887	2077	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107455.1	s__Asanoa ishikariensis	86.3135	2076	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003387075.1	s__Asanoa ferruginea	85.6712	1965	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900091455.1	s__Micromonospora coriariae	79.5827	1112	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030345.1	s__Plantactinospora sp003030345	79.4522	1235	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_900090245.1	s__Micromonospora halophytica	79.4219	1056	2823	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:36,811] [INFO] GTDB search result was written to GCF_016862555.1_ASM1686255v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:36,813] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:36,815] [INFO] DFAST_QC result json was written to GCF_016862555.1_ASM1686255v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:36,815] [INFO] DFAST_QC completed!
[2024-01-25 18:05:36,815] [INFO] Total running time: 0h2m16s