[2024-01-24 13:22:10,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,144] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference
[2024-01-24 13:22:11,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,521] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,522] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6697597-ba81-4be2-be7e-ef771ad5ea12/GCF_003933745.1_ASM393374v1_genomic.fna.gz | prodigal -d GCF_003933745.1_ASM393374v1_genomic.fna/cds.fna -a GCF_003933745.1_ASM393374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:25,795] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:25,796] [INFO] Task started: HMMsearch
[2024-01-24 13:22:25,796] [INFO] Running command: hmmsearch --tblout GCF_003933745.1_ASM393374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference/reference_markers.hmm GCF_003933745.1_ASM393374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:26,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:26,139] [INFO] Found 6/6 markers.
[2024-01-24 13:22:26,185] [INFO] Query marker FASTA was written to GCF_003933745.1_ASM393374v1_genomic.fna/markers.fasta
[2024-01-24 13:22:26,186] [INFO] Task started: Blastn
[2024-01-24 13:22:26,186] [INFO] Running command: blastn -query GCF_003933745.1_ASM393374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference/reference_markers.fasta -out GCF_003933745.1_ASM393374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:27,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:27,489] [INFO] Selected 5 target genomes.
[2024-01-24 13:22:27,489] [INFO] Target genome list was writen to GCF_003933745.1_ASM393374v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:27,495] [INFO] Task started: fastANI
[2024-01-24 13:22:27,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6697597-ba81-4be2-be7e-ef771ad5ea12/GCF_003933745.1_ASM393374v1_genomic.fna.gz --refList GCF_003933745.1_ASM393374v1_genomic.fna/target_genomes.txt --output GCF_003933745.1_ASM393374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:36,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:36,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:36,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:36,865] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:36,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:36,865] [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 terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	100.0	1737	1739	95	conclusive
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	90.2484	1286	1739	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	89.9763	1436	1739	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	89.4303	1439	1739	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	89.0751	1414	1739	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,866] [INFO] DFAST Taxonomy check result was written to GCF_003933745.1_ASM393374v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:36,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:36,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:36,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference/checkm_data
[2024-01-24 13:22:36,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:36,924] [INFO] Task started: CheckM
[2024-01-24 13:22:36,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003933745.1_ASM393374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003933745.1_ASM393374v1_genomic.fna/checkm_input GCF_003933745.1_ASM393374v1_genomic.fna/checkm_result
[2024-01-24 13:23:36,561] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:36,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,587] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:36,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:36,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003933745.1_ASM393374v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:36,588] [INFO] Task started: Blastn
[2024-01-24 13:23:36,588] [INFO] Running command: blastn -query GCF_003933745.1_ASM393374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09441314-2b4e-4a21-a85e-5a719d759eb8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003933745.1_ASM393374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:38,474] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:38,478] [INFO] Selected 5 target genomes.
[2024-01-24 13:23:38,478] [INFO] Target genome list was writen to GCF_003933745.1_ASM393374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:38,483] [INFO] Task started: fastANI
[2024-01-24 13:23:38,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6697597-ba81-4be2-be7e-ef771ad5ea12/GCF_003933745.1_ASM393374v1_genomic.fna.gz --refList GCF_003933745.1_ASM393374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003933745.1_ASM393374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:47,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:47,552] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:47,552] [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_003933745.1	s__Glycomyces terrestris	100.0	1737	1739	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_003265355.1	s__Glycomyces dulcitolivorans	90.2819	1282	1739	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	89.9761	1436	1739	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	89.4443	1438	1739	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	89.0702	1414	1739	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:47,554] [INFO] GTDB search result was written to GCF_003933745.1_ASM393374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:47,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:47,556] [INFO] DFAST_QC result json was written to GCF_003933745.1_ASM393374v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:47,557] [INFO] DFAST_QC completed!
[2024-01-24 13:23:47,557] [INFO] Total running time: 0h1m37s