[2024-01-24 13:40:33,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference
[2024-01-24 13:40:34,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,540] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg5185faad-0bc2-45bd-afae-13c5e15c1b9c/GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/cds.fna -a GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:51,007] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:51,008] [INFO] Task started: HMMsearch
[2024-01-24 13:40:51,008] [INFO] Running command: hmmsearch --tblout GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference/reference_markers.hmm GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,323] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,371] [INFO] Query marker FASTA was written to GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:51,371] [INFO] Task started: Blastn
[2024-01-24 13:40:51,372] [INFO] Running command: blastn -query GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference/reference_markers.fasta -out GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,719] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:52,720] [INFO] Target genome list was writen to GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,728] [INFO] Task started: fastANI
[2024-01-24 13:40:52,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg5185faad-0bc2-45bd-afae-13c5e15c1b9c/GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna.gz --refList GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:06,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:06,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:06,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:06,592] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:06,592] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:06,592] [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 alba	strain=DSM 45004	GCA_900112765.1	673379	673379	type	True	92.926	1427	1655	95	below_threshold
Actinopolyspora righensis	strain=DSM 45501	GCA_900116555.1	995060	995060	type	True	92.7646	1410	1655	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_000763095.1	414996	414996	type	True	86.4501	1304	1655	95	below_threshold
Actinopolyspora erythraea	strain=YIM 90600	GCA_002263515.1	414996	414996	type	True	86.4466	1313	1655	95	below_threshold
Actinopolyspora xinjiangensis	strain=DSM 46732	GCA_900104475.1	405564	405564	type	True	86.1648	1302	1655	95	below_threshold
Actinopolyspora biskrensis	strain=CECT 8576	GCA_013408175.1	1470178	1470178	type	True	81.6863	976	1655	95	below_threshold
Saccharopolyspora subtropica	strain=CGMCC 4.7206	GCA_014646075.1	1530170	1530170	type	True	78.8183	588	1655	95	below_threshold
Saccharopolyspora kobensis	strain=ATCC 20501	GCA_900108315.1	146035	146035	type	True	78.7147	647	1655	95	below_threshold
Saccharopolyspora rectivirgula	strain=DSM 43747	GCA_000497205.1	28042	28042	type	True	78.4115	490	1655	95	below_threshold
Pseudonocardia hydrocarbonoxydans	strain=NBRC 14498	GCA_006539565.1	76726	76726	type	True	76.78	334	1655	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	76.6966	395	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,594] [INFO] DFAST Taxonomy check result was written to GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:06,595] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:06,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:06,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference/checkm_data
[2024-01-24 13:41:06,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:06,647] [INFO] Task started: CheckM
[2024-01-24 13:41:06,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/checkm_input GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:55,919] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:55,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:55,946] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:55,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:55,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:55,947] [INFO] Task started: Blastn
[2024-01-24 13:41:55,947] [INFO] Running command: blastn -query GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aae9dfe-160c-4bc1-abb5-0c665fd40c75/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:57,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:57,747] [INFO] Selected 8 target genomes.
[2024-01-24 13:41:57,747] [INFO] Target genome list was writen to GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:57,754] [INFO] Task started: fastANI
[2024-01-24 13:41:57,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg5185faad-0bc2-45bd-afae-13c5e15c1b9c/GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna.gz --refList GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:08,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:08,889] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:08,890] [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_900101095.1	s__Actinopolyspora mzabensis	100.0	1654	1655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112765.1	s__Actinopolyspora alba	92.9284	1426	1655	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	92.7534	1411	1655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.8717	98.44	98.44	0.91	0.91	2	-
GCF_002263515.1	s__Actinopolyspora erythraea	86.4536	1312	1655	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	86.1738	1301	1655	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	81.7677	1002	1655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	98.98	98.97	0.92	0.92	3	-
GCF_000371785.1	s__Actinopolyspora halophila	81.7284	984	1655	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	81.7076	969	1655	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:08,899] [INFO] GTDB search result was written to GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:08,900] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:08,905] [INFO] DFAST_QC result json was written to GCF_900101095.1_IMG-taxon_2619619027_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:08,906] [INFO] DFAST_QC completed!
[2024-01-24 13:42:08,906] [INFO] Total running time: 0h1m36s