[2024-01-24 13:01:10,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:10,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:10,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference
[2024-01-24 13:01:11,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:11,856] [INFO] Task started: Prodigal
[2024-01-24 13:01:11,856] [INFO] Running command: gunzip -c /var/lib/cwl/stged555822-fd61-4013-bea5-c3d48f8bb668/GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/cds.fna -a GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:26,428] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:26,429] [INFO] Task started: HMMsearch
[2024-01-24 13:01:26,429] [INFO] Running command: hmmsearch --tblout GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference/reference_markers.hmm GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:26,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:26,800] [INFO] Found 6/6 markers.
[2024-01-24 13:01:26,840] [INFO] Query marker FASTA was written to GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:26,840] [INFO] Task started: Blastn
[2024-01-24 13:01:26,841] [INFO] Running command: blastn -query GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference/reference_markers.fasta -out GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:28,006] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:28,010] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:28,010] [INFO] Target genome list was writen to GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:28,016] [INFO] Task started: fastANI
[2024-01-24 13:01:28,016] [INFO] Running command: fastANI --query /var/lib/cwl/stged555822-fd61-4013-bea5-c3d48f8bb668/GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna.gz --refList GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:45,163] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:45,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:45,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:45,175] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:45,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:45,176] [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 saharensis	strain=DSM 45459	GCA_900100925.1	995062	995062	type	True	100.0	1556	1560	95	conclusive
Actinopolyspora halophila	strain=DSM 43834	GCA_000371785.1	1850	1850	type	True	92.2762	1420	1560	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	91.764	1320	1560	95	below_threshold
Actinopolyspora mortivallis	strain=HS-1	GCA_000384035.1	33906	33906	type	True	83.2341	1052	1560	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	82.2984	1043	1560	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	82.2923	1033	1560	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	82.1521	1024	1560	95	below_threshold
Actinopolyspora alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	81.9191	1001	1560	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	81.9108	974	1560	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	78.8307	672	1560	95	below_threshold
Saccharopolyspora rectivirgula	strain=DSM 43747	GCA_000497205.1	28042	28042	type	True	78.6655	483	1560	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	76.8396	395	1560	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	76.6895	416	1560	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	76.6518	440	1560	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:45,177] [INFO] DFAST Taxonomy check result was written to GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:45,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:45,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:45,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference/checkm_data
[2024-01-24 13:01:45,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:45,223] [INFO] Task started: CheckM
[2024-01-24 13:01:45,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/checkm_input GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:31,788] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:31,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:31,809] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:31,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:31,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:31,810] [INFO] Task started: Blastn
[2024-01-24 13:02:31,810] [INFO] Running command: blastn -query GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af9ece9-f082-4c5c-924a-a57cfc32c6f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:33,448] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:33,452] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:33,452] [INFO] Target genome list was writen to GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:33,458] [INFO] Task started: fastANI
[2024-01-24 13:02:33,458] [INFO] Running command: fastANI --query /var/lib/cwl/stged555822-fd61-4013-bea5-c3d48f8bb668/GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna.gz --refList GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:44,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:44,573] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:44,574] [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_900100925.1	s__Actinopolyspora saharensis	100.0	1559	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	conclusive
GCF_000371785.1	s__Actinopolyspora halophila	92.2966	1417	1560	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	92.0625	1376	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408175.1	s__Actinopolyspora biskrensis	91.764	1320	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384035.1	s__Actinopolyspora mortivallis	83.2372	1050	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	95.34	95.34	0.86	0.86	2	-
GCF_002263515.1	s__Actinopolyspora erythraea	82.3249	1043	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900104475.1	s__Actinopolyspora xinjiangensis	82.1588	1022	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112765.1	s__Actinopolyspora alba	81.9284	999	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	N/A	N/A	N/A	N/A	1	-
GCF_900116555.1	s__Actinopolyspora righensis	81.8909	976	1560	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,575] [INFO] GTDB search result was written to GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:44,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:44,580] [INFO] DFAST_QC result json was written to GCF_900100925.1_IMG-taxon_2634166628_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:44,580] [INFO] DFAST_QC completed!
[2024-01-24 13:02:44,580] [INFO] Total running time: 0h1m34s