[2024-01-24 12:21:44,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference
[2024-01-24 12:21:45,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,467] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg47cd4659-3c06-45bb-8927-f941321835b6/GCF_031458375.1_ASM3145837v1_genomic.fna.gz | prodigal -d GCF_031458375.1_ASM3145837v1_genomic.fna/cds.fna -a GCF_031458375.1_ASM3145837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:01,033] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:01,034] [INFO] Task started: HMMsearch
[2024-01-24 12:22:01,034] [INFO] Running command: hmmsearch --tblout GCF_031458375.1_ASM3145837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference/reference_markers.hmm GCF_031458375.1_ASM3145837v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:01,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:01,423] [INFO] Found 6/6 markers.
[2024-01-24 12:22:01,466] [INFO] Query marker FASTA was written to GCF_031458375.1_ASM3145837v1_genomic.fna/markers.fasta
[2024-01-24 12:22:01,466] [INFO] Task started: Blastn
[2024-01-24 12:22:01,466] [INFO] Running command: blastn -query GCF_031458375.1_ASM3145837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference/reference_markers.fasta -out GCF_031458375.1_ASM3145837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:02,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:02,716] [INFO] Selected 6 target genomes.
[2024-01-24 12:22:02,716] [INFO] Target genome list was writen to GCF_031458375.1_ASM3145837v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:02,719] [INFO] Task started: fastANI
[2024-01-24 12:22:02,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg47cd4659-3c06-45bb-8927-f941321835b6/GCF_031458375.1_ASM3145837v1_genomic.fna.gz --refList GCF_031458375.1_ASM3145837v1_genomic.fna/target_genomes.txt --output GCF_031458375.1_ASM3145837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:12,001] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:12,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:12,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:12,010] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:12,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:12,011] [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	85.6767	1203	1853	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	85.5739	1270	1853	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	85.5148	1273	1853	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	85.4708	1311	1853	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	85.4355	1352	1853	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	85.2356	1337	1853	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:12,013] [INFO] DFAST Taxonomy check result was written to GCF_031458375.1_ASM3145837v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:12,016] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:12,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:12,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference/checkm_data
[2024-01-24 12:22:12,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:12,077] [INFO] Task started: CheckM
[2024-01-24 12:22:12,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458375.1_ASM3145837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458375.1_ASM3145837v1_genomic.fna/checkm_input GCF_031458375.1_ASM3145837v1_genomic.fna/checkm_result
[2024-01-24 12:23:04,776] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:04,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:04,805] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:04,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:04,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458375.1_ASM3145837v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:04,807] [INFO] Task started: Blastn
[2024-01-24 12:23:04,807] [INFO] Running command: blastn -query GCF_031458375.1_ASM3145837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a4eefe7-6530-4ddc-bfae-157c607b5244/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458375.1_ASM3145837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:06,821] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:06,826] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:06,826] [INFO] Target genome list was writen to GCF_031458375.1_ASM3145837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:06,834] [INFO] Task started: fastANI
[2024-01-24 12:23:06,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg47cd4659-3c06-45bb-8927-f941321835b6/GCF_031458375.1_ASM3145837v1_genomic.fna.gz --refList GCF_031458375.1_ASM3145837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458375.1_ASM3145837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:20,928] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,936] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:20,936] [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	89.541	1428	1853	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	89.2217	1427	1853	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	86.0195	1353	1853	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	85.6643	1204	1853	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	85.5648	1271	1853	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	85.5167	1274	1853	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	85.4913	1308	1853	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	85.4093	1357	1853	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	85.4043	1192	1853	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 12:23:20,938] [INFO] GTDB search result was written to GCF_031458375.1_ASM3145837v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:20,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:20,941] [INFO] DFAST_QC result json was written to GCF_031458375.1_ASM3145837v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:20,941] [INFO] DFAST_QC completed!
[2024-01-24 12:23:20,941] [INFO] Total running time: 0h1m37s