[2024-01-24 13:49:27,519] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,526] [INFO] DQC Reference Directory: /var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference
[2024-01-24 13:49:28,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,864] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b5ba958-898c-4ceb-9ded-86ec4cfa3c81/GCF_004912155.1_ASM491215v1_genomic.fna.gz | prodigal -d GCF_004912155.1_ASM491215v1_genomic.fna/cds.fna -a GCF_004912155.1_ASM491215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:44,423] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:44,424] [INFO] Task started: HMMsearch
[2024-01-24 13:49:44,424] [INFO] Running command: hmmsearch --tblout GCF_004912155.1_ASM491215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference/reference_markers.hmm GCF_004912155.1_ASM491215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:44,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:44,775] [INFO] Found 6/6 markers.
[2024-01-24 13:49:44,825] [INFO] Query marker FASTA was written to GCF_004912155.1_ASM491215v1_genomic.fna/markers.fasta
[2024-01-24 13:49:44,825] [INFO] Task started: Blastn
[2024-01-24 13:49:44,825] [INFO] Running command: blastn -query GCF_004912155.1_ASM491215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference/reference_markers.fasta -out GCF_004912155.1_ASM491215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:46,081] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:46,090] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:46,090] [INFO] Target genome list was writen to GCF_004912155.1_ASM491215v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:46,097] [INFO] Task started: fastANI
[2024-01-24 13:49:46,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b5ba958-898c-4ceb-9ded-86ec4cfa3c81/GCF_004912155.1_ASM491215v1_genomic.fna.gz --refList GCF_004912155.1_ASM491215v1_genomic.fna/target_genomes.txt --output GCF_004912155.1_ASM491215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:56,190] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:56,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:56,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:56,198] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:56,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:56,199] [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 paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	100.0	1777	1779	95	conclusive
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	86.1694	1160	1779	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	86.0453	1288	1779	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	85.9764	1246	1779	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	85.8774	1277	1779	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	85.5655	1236	1779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,201] [INFO] DFAST Taxonomy check result was written to GCF_004912155.1_ASM491215v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:56,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:56,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:56,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference/checkm_data
[2024-01-24 13:49:56,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:56,259] [INFO] Task started: CheckM
[2024-01-24 13:49:56,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004912155.1_ASM491215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004912155.1_ASM491215v1_genomic.fna/checkm_input GCF_004912155.1_ASM491215v1_genomic.fna/checkm_result
[2024-01-24 13:50:57,783] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:57,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:57,806] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:57,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:57,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004912155.1_ASM491215v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:57,808] [INFO] Task started: Blastn
[2024-01-24 13:50:57,808] [INFO] Running command: blastn -query GCF_004912155.1_ASM491215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf363ab63-1e4b-4672-969d-ed6a481efbb1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004912155.1_ASM491215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:59,510] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:59,514] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:59,514] [INFO] Target genome list was writen to GCF_004912155.1_ASM491215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:59,524] [INFO] Task started: fastANI
[2024-01-24 13:50:59,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b5ba958-898c-4ceb-9ded-86ec4cfa3c81/GCF_004912155.1_ASM491215v1_genomic.fna.gz --refList GCF_004912155.1_ASM491215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004912155.1_ASM491215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:13,183] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:13,192] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:13,192] [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_004912155.1	s__Glycomyces paridis	100.0	1777	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000719515.1	s__Glycomyces sp000719515	87.3949	1274	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900101745.1	s__Glycomyces harbinensis	86.2942	1325	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265355.1	s__Glycomyces dulcitolivorans	86.1662	1161	1779	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	86.0195	1291	1779	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	85.9844	1245	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002955.1	s__Glycomyces artemisiae	85.8212	1284	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
GCF_017592475.1	s__Glycomyces sp017592475	85.6639	1204	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918015.1	s__Glycomyces sp016918015	85.1904	1208	1779	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,195] [INFO] GTDB search result was written to GCF_004912155.1_ASM491215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:13,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:13,200] [INFO] DFAST_QC result json was written to GCF_004912155.1_ASM491215v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:13,201] [INFO] DFAST_QC completed!
[2024-01-24 13:51:13,201] [INFO] Total running time: 0h1m46s