[2024-01-24 12:13:28,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,508] [INFO] DQC Reference Directory: /var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference
[2024-01-24 12:13:29,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,907] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg345272f8-e451-46b3-bbab-689e71f0124e/GCF_003387075.1_ASM338707v1_genomic.fna.gz | prodigal -d GCF_003387075.1_ASM338707v1_genomic.fna/cds.fna -a GCF_003387075.1_ASM338707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:56,912] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:56,913] [INFO] Task started: HMMsearch
[2024-01-24 12:13:56,913] [INFO] Running command: hmmsearch --tblout GCF_003387075.1_ASM338707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference/reference_markers.hmm GCF_003387075.1_ASM338707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:57,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:57,418] [INFO] Found 6/6 markers.
[2024-01-24 12:13:57,493] [INFO] Query marker FASTA was written to GCF_003387075.1_ASM338707v1_genomic.fna/markers.fasta
[2024-01-24 12:13:57,493] [INFO] Task started: Blastn
[2024-01-24 12:13:57,494] [INFO] Running command: blastn -query GCF_003387075.1_ASM338707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference/reference_markers.fasta -out GCF_003387075.1_ASM338707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:58,827] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:58,840] [INFO] Selected 8 target genomes.
[2024-01-24 12:13:58,841] [INFO] Target genome list was writen to GCF_003387075.1_ASM338707v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:58,845] [INFO] Task started: fastANI
[2024-01-24 12:13:58,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg345272f8-e451-46b3-bbab-689e71f0124e/GCF_003387075.1_ASM338707v1_genomic.fna.gz --refList GCF_003387075.1_ASM338707v1_genomic.fna/target_genomes.txt --output GCF_003387075.1_ASM338707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:20,252] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:20,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:20,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:20,260] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:20,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:20,260] [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 ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	100.0	3023	3023	95	conclusive
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	99.9554	2898	3023	95	conclusive
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	86.1434	2194	3023	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	86.1339	2185	3023	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	85.9246	2076	3023	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	85.7982	2053	3023	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	85.5569	1976	3023	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	77.7735	1149	3023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:20,282] [INFO] DFAST Taxonomy check result was written to GCF_003387075.1_ASM338707v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:20,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:20,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:20,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference/checkm_data
[2024-01-24 12:14:20,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:20,373] [INFO] Task started: CheckM
[2024-01-24 12:14:20,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003387075.1_ASM338707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003387075.1_ASM338707v1_genomic.fna/checkm_input GCF_003387075.1_ASM338707v1_genomic.fna/checkm_result
[2024-01-24 12:15:52,569] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:52,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:52,602] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:52,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:52,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003387075.1_ASM338707v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:52,603] [INFO] Task started: Blastn
[2024-01-24 12:15:52,603] [INFO] Running command: blastn -query GCF_003387075.1_ASM338707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd675e0da-97e2-4ce4-83e3-43b38f2f7b62/dqc_reference/reference_markers_gtdb.fasta -out GCF_003387075.1_ASM338707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:54,379] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:54,383] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:54,383] [INFO] Target genome list was writen to GCF_003387075.1_ASM338707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:54,388] [INFO] Task started: fastANI
[2024-01-24 12:15:54,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg345272f8-e451-46b3-bbab-689e71f0124e/GCF_003387075.1_ASM338707v1_genomic.fna.gz --refList GCF_003387075.1_ASM338707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003387075.1_ASM338707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:11,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:11,725] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:11,726] [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_003387075.1	s__Asanoa ferruginea	100.0	3022	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900107455.1	s__Asanoa ishikariensis	86.1257	2196	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188485.1	s__Asanoa hainanensis	85.9221	2075	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862515.1	s__Asanoa iriomotensis	85.7627	2059	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862555.1	s__Asanoa siamensis	85.5492	1979	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	78.1758	1027	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	77.7519	1158	3023	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:11,727] [INFO] GTDB search result was written to GCF_003387075.1_ASM338707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:11,728] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:11,732] [INFO] DFAST_QC result json was written to GCF_003387075.1_ASM338707v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:11,732] [INFO] DFAST_QC completed!
[2024-01-24 12:16:11,732] [INFO] Total running time: 0h2m43s