[2024-01-24 13:21:59,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:59,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:59,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference
[2024-01-24 13:22:01,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:01,051] [INFO] Task started: Prodigal
[2024-01-24 13:22:01,051] [INFO] Running command: gunzip -c /var/lib/cwl/stge3c639c8-b422-4294-b304-e66fcbc2862b/GCF_030403505.1_ASM3040350v1_genomic.fna.gz | prodigal -d GCF_030403505.1_ASM3040350v1_genomic.fna/cds.fna -a GCF_030403505.1_ASM3040350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:19,755] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:19,755] [INFO] Task started: HMMsearch
[2024-01-24 13:22:19,756] [INFO] Running command: hmmsearch --tblout GCF_030403505.1_ASM3040350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference/reference_markers.hmm GCF_030403505.1_ASM3040350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:20,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:20,160] [INFO] Found 6/6 markers.
[2024-01-24 13:22:20,214] [INFO] Query marker FASTA was written to GCF_030403505.1_ASM3040350v1_genomic.fna/markers.fasta
[2024-01-24 13:22:20,215] [INFO] Task started: Blastn
[2024-01-24 13:22:20,215] [INFO] Running command: blastn -query GCF_030403505.1_ASM3040350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference/reference_markers.fasta -out GCF_030403505.1_ASM3040350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:21,667] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:21,670] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:21,670] [INFO] Target genome list was writen to GCF_030403505.1_ASM3040350v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:21,675] [INFO] Task started: fastANI
[2024-01-24 13:22:21,675] [INFO] Running command: fastANI --query /var/lib/cwl/stge3c639c8-b422-4294-b304-e66fcbc2862b/GCF_030403505.1_ASM3040350v1_genomic.fna.gz --refList GCF_030403505.1_ASM3040350v1_genomic.fna/target_genomes.txt --output GCF_030403505.1_ASM3040350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:31,988] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:31,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:31,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:31,996] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:31,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:31,996] [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	85.7565	1311	2136	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	85.6991	1195	2136	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	85.6336	1280	2136	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	85.6218	1326	2136	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	85.5207	1251	2136	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	85.295	1307	2136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:31,998] [INFO] DFAST Taxonomy check result was written to GCF_030403505.1_ASM3040350v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:31,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:31,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:31,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference/checkm_data
[2024-01-24 13:22:32,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:32,068] [INFO] Task started: CheckM
[2024-01-24 13:22:32,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030403505.1_ASM3040350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030403505.1_ASM3040350v1_genomic.fna/checkm_input GCF_030403505.1_ASM3040350v1_genomic.fna/checkm_result
[2024-01-24 13:23:28,826] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:28,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:28,846] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:28,846] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:28,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030403505.1_ASM3040350v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:28,847] [INFO] Task started: Blastn
[2024-01-24 13:23:28,847] [INFO] Running command: blastn -query GCF_030403505.1_ASM3040350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59b0dc03-5fd7-4867-93a2-f92fb3c4f5b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_030403505.1_ASM3040350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:30,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:30,863] [INFO] Selected 8 target genomes.
[2024-01-24 13:23:30,863] [INFO] Target genome list was writen to GCF_030403505.1_ASM3040350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:30,883] [INFO] Task started: fastANI
[2024-01-24 13:23:30,883] [INFO] Running command: fastANI --query /var/lib/cwl/stge3c639c8-b422-4294-b304-e66fcbc2862b/GCF_030403505.1_ASM3040350v1_genomic.fna.gz --refList GCF_030403505.1_ASM3040350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030403505.1_ASM3040350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:43,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:43,806] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:23:43,807] [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_016918015.1	s__Glycomyces sp016918015	89.8338	1435	2136	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	89.439	1431	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101745.1	s__Glycomyces harbinensis	85.9338	1345	2136	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	85.6916	1196	2136	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	85.6778	1320	2136	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	85.5831	1286	2136	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	85.4904	1256	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719515.1	s__Glycomyces sp000719515	85.3932	1182	2136	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:43,808] [INFO] GTDB search result was written to GCF_030403505.1_ASM3040350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:43,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:43,811] [INFO] DFAST_QC result json was written to GCF_030403505.1_ASM3040350v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:43,811] [INFO] DFAST_QC completed!
[2024-01-24 13:23:43,811] [INFO] Total running time: 0h1m44s