[2024-01-24 13:10:04,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:04,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:04,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference
[2024-01-24 13:10:05,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,418] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgaab01645-95c9-48ee-bad0-8e743eaca75f/GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/cds.fna -a GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:20,783] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:20,783] [INFO] Task started: HMMsearch
[2024-01-24 13:10:20,783] [INFO] Running command: hmmsearch --tblout GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference/reference_markers.hmm GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:21,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:21,126] [INFO] Found 6/6 markers.
[2024-01-24 13:10:21,166] [INFO] Query marker FASTA was written to GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:10:21,167] [INFO] Task started: Blastn
[2024-01-24 13:10:21,167] [INFO] Running command: blastn -query GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference/reference_markers.fasta -out GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:22,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:22,362] [INFO] Selected 6 target genomes.
[2024-01-24 13:10:22,363] [INFO] Target genome list was writen to GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:10:22,366] [INFO] Task started: fastANI
[2024-01-24 13:10:22,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgaab01645-95c9-48ee-bad0-8e743eaca75f/GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna.gz --refList GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:31,851] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:31,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:31,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:31,863] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:10:31,863] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:10:31,863] [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 righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	100.0	1630	1631	95	inconclusive
Actinopolyspora alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	95.8631	1484	1631	95	inconclusive
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	87.0869	1345	1631	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	87.0841	1348	1631	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	86.4495	1325	1631	95	below_threshold
Actinopolyspora saharensis	strain=DSM 45459	GCA_900100925.1	995062	995062	type	True	81.8372	987	1631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:31,865] [INFO] DFAST Taxonomy check result was written to GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:31,865] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:31,865] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:31,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference/checkm_data
[2024-01-24 13:10:31,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:31,916] [INFO] Task started: CheckM
[2024-01-24 13:10:31,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/checkm_input GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:11:19,470] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:19,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:19,499] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:19,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:19,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:11:19,501] [INFO] Task started: Blastn
[2024-01-24 13:11:19,501] [INFO] Running command: blastn -query GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9157962c-add3-49f0-806d-8571fca8ace6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:21,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:21,165] [INFO] Selected 6 target genomes.
[2024-01-24 13:11:21,165] [INFO] Target genome list was writen to GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:21,171] [INFO] Task started: fastANI
[2024-01-24 13:11:21,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgaab01645-95c9-48ee-bad0-8e743eaca75f/GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna.gz --refList GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:29,890] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:29,902] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:29,902] [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_900116555.1	s__Actinopolyspora righensis	100.0	1630	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	conclusive
GCF_900112765.1	s__Actinopolyspora alba	95.8717	1483	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101095.1	s__Actinopolyspora mzabensis	92.7994	1420	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263515.1	s__Actinopolyspora erythraea	87.0834	1346	1631	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	86.4581	1323	1631	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	81.8401	986	1631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:29,904] [INFO] GTDB search result was written to GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:29,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:29,909] [INFO] DFAST_QC result json was written to GCF_900116555.1_IMG-taxon_2616644808_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:11:29,909] [INFO] DFAST_QC completed!
[2024-01-24 13:11:29,909] [INFO] Total running time: 0h1m26s