[2024-01-25 18:15:35,563] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference
[2024-01-25 18:15:36,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,665] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,665] [INFO] Running command: gunzip -c /var/lib/cwl/stg51a0f2c1-18f6-4174-8d9e-b293863538d7/GCF_003002955.1_ASM300295v1_genomic.fna.gz | prodigal -d GCF_003002955.1_ASM300295v1_genomic.fna/cds.fna -a GCF_003002955.1_ASM300295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:50,079] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:50,080] [INFO] Task started: HMMsearch
[2024-01-25 18:15:50,080] [INFO] Running command: hmmsearch --tblout GCF_003002955.1_ASM300295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference/reference_markers.hmm GCF_003002955.1_ASM300295v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:50,380] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:50,381] [INFO] Found 6/6 markers.
[2024-01-25 18:15:50,430] [INFO] Query marker FASTA was written to GCF_003002955.1_ASM300295v1_genomic.fna/markers.fasta
[2024-01-25 18:15:50,430] [INFO] Task started: Blastn
[2024-01-25 18:15:50,430] [INFO] Running command: blastn -query GCF_003002955.1_ASM300295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference/reference_markers.fasta -out GCF_003002955.1_ASM300295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:51,579] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:51,583] [INFO] Selected 11 target genomes.
[2024-01-25 18:15:51,583] [INFO] Target genome list was writen to GCF_003002955.1_ASM300295v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:51,602] [INFO] Task started: fastANI
[2024-01-25 18:15:51,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg51a0f2c1-18f6-4174-8d9e-b293863538d7/GCF_003002955.1_ASM300295v1_genomic.fna.gz --refList GCF_003002955.1_ASM300295v1_genomic.fna/target_genomes.txt --output GCF_003002955.1_ASM300295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:08,759] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:08,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:08,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:08,769] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:08,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:08,770] [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
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	100.0	1910	1914	95	conclusive
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	89.517	1356	1914	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	89.2499	1482	1914	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	88.9577	1418	1914	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	88.1894	1419	1914	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	85.8882	1277	1914	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	76.1879	547	1914	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	76.047	525	1914	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	76.0118	522	1914	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	75.9902	561	1914	95	below_threshold
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	75.9566	565	1914	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:08,771] [INFO] DFAST Taxonomy check result was written to GCF_003002955.1_ASM300295v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:08,772] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:08,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:08,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference/checkm_data
[2024-01-25 18:16:08,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:08,832] [INFO] Task started: CheckM
[2024-01-25 18:16:08,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002955.1_ASM300295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002955.1_ASM300295v1_genomic.fna/checkm_input GCF_003002955.1_ASM300295v1_genomic.fna/checkm_result
[2024-01-25 18:16:53,220] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:53,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:53,243] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:53,243] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:53,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002955.1_ASM300295v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:53,244] [INFO] Task started: Blastn
[2024-01-25 18:16:53,244] [INFO] Running command: blastn -query GCF_003002955.1_ASM300295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6f52310-e763-48d3-9fcc-e9d626ae416f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002955.1_ASM300295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:54,947] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:54,949] [INFO] Selected 11 target genomes.
[2024-01-25 18:16:54,949] [INFO] Target genome list was writen to GCF_003002955.1_ASM300295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:54,963] [INFO] Task started: fastANI
[2024-01-25 18:16:54,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg51a0f2c1-18f6-4174-8d9e-b293863538d7/GCF_003002955.1_ASM300295v1_genomic.fna.gz --refList GCF_003002955.1_ASM300295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002955.1_ASM300295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:11,885] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:11,892] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:11,893] [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_003002955.1	s__Glycomyces artemisiae	100.0	1910	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	conclusive
GCF_003265355.1	s__Glycomyces dulcitolivorans	89.5391	1354	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102815.1	s__Glycomyces sambucus	89.3084	1475	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933745.1	s__Glycomyces terrestris	88.9292	1421	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009451885.1	s__Glycomyces albidus	88.205	1416	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912155.1	s__Glycomyces paridis	85.9032	1275	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592475.1	s__Glycomyces sp017592475	85.6159	1293	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720635.1	s__Kitasatospora sp000720635	76.1066	561	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918855.1	s__Streptomyces acididurans	76.0487	521	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718635.1	s__Streptomyces varsoviensis	75.9715	560	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001898805.1	s__Leifsonia sp001898805	75.8808	350	1914	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leifsonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:11,894] [INFO] GTDB search result was written to GCF_003002955.1_ASM300295v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:11,894] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:11,897] [INFO] DFAST_QC result json was written to GCF_003002955.1_ASM300295v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:11,897] [INFO] DFAST_QC completed!
[2024-01-25 18:17:11,897] [INFO] Total running time: 0h1m36s