[2024-01-24 12:37:37,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference
[2024-01-24 12:37:41,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,019] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg63cf5027-610f-4b6d-83ff-d1a4c3a47c19/GCF_003265355.1_ASM326535v1_genomic.fna.gz | prodigal -d GCF_003265355.1_ASM326535v1_genomic.fna/cds.fna -a GCF_003265355.1_ASM326535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:54,536] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:54,536] [INFO] Task started: HMMsearch
[2024-01-24 12:37:54,536] [INFO] Running command: hmmsearch --tblout GCF_003265355.1_ASM326535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference/reference_markers.hmm GCF_003265355.1_ASM326535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:54,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:54,853] [INFO] Found 6/6 markers.
[2024-01-24 12:37:54,905] [INFO] Query marker FASTA was written to GCF_003265355.1_ASM326535v1_genomic.fna/markers.fasta
[2024-01-24 12:37:54,906] [INFO] Task started: Blastn
[2024-01-24 12:37:54,906] [INFO] Running command: blastn -query GCF_003265355.1_ASM326535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference/reference_markers.fasta -out GCF_003265355.1_ASM326535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:56,104] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:56,108] [INFO] Selected 6 target genomes.
[2024-01-24 12:37:56,108] [INFO] Target genome list was writen to GCF_003265355.1_ASM326535v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:56,113] [INFO] Task started: fastANI
[2024-01-24 12:37:56,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg63cf5027-610f-4b6d-83ff-d1a4c3a47c19/GCF_003265355.1_ASM326535v1_genomic.fna.gz --refList GCF_003265355.1_ASM326535v1_genomic.fna/target_genomes.txt --output GCF_003265355.1_ASM326535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:05,666] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:05,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:05,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:05,674] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:05,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:05,674] [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 dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	100.0	1725	1736	95	conclusive
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	90.5595	1364	1736	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	90.1564	1306	1736	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	89.5578	1384	1736	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	89.126	1317	1736	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	86.0942	1170	1736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:05,679] [INFO] DFAST Taxonomy check result was written to GCF_003265355.1_ASM326535v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:05,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:05,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:05,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference/checkm_data
[2024-01-24 12:38:05,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:05,755] [INFO] Task started: CheckM
[2024-01-24 12:38:05,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003265355.1_ASM326535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003265355.1_ASM326535v1_genomic.fna/checkm_input GCF_003265355.1_ASM326535v1_genomic.fna/checkm_result
[2024-01-24 12:38:48,320] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:48,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:48,345] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:48,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:48,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003265355.1_ASM326535v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:48,347] [INFO] Task started: Blastn
[2024-01-24 12:38:48,347] [INFO] Running command: blastn -query GCF_003265355.1_ASM326535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e96c518-e72a-418b-9ec1-db1cdc3d1dfb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003265355.1_ASM326535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:50,153] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:50,158] [INFO] Selected 6 target genomes.
[2024-01-24 12:38:50,158] [INFO] Target genome list was writen to GCF_003265355.1_ASM326535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:50,168] [INFO] Task started: fastANI
[2024-01-24 12:38:50,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg63cf5027-610f-4b6d-83ff-d1a4c3a47c19/GCF_003265355.1_ASM326535v1_genomic.fna.gz --refList GCF_003265355.1_ASM326535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003265355.1_ASM326535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:59,717] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:59,730] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:59,730] [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_003265355.1	s__Glycomyces dulcitolivorans	100.0	1725	1736	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_900102815.1	s__Glycomyces sambucus	90.575	1362	1736	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	90.2269	1300	1736	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	89.5215	1387	1736	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
GCF_009451885.1	s__Glycomyces albidus	89.1371	1316	1736	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	86.0704	1171	1736	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 12:38:59,733] [INFO] GTDB search result was written to GCF_003265355.1_ASM326535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:59,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:59,738] [INFO] DFAST_QC result json was written to GCF_003265355.1_ASM326535v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:59,739] [INFO] DFAST_QC completed!
[2024-01-24 12:38:59,739] [INFO] Total running time: 0h1m22s