[2024-01-24 13:46:18,585] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference
[2024-01-24 13:46:19,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,867] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbe15ce9-7d38-4a60-ab29-7184cc4c11f4/GCF_031458295.1_ASM3145829v1_genomic.fna.gz | prodigal -d GCF_031458295.1_ASM3145829v1_genomic.fna/cds.fna -a GCF_031458295.1_ASM3145829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:36,482] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:36,483] [INFO] Task started: HMMsearch
[2024-01-24 13:46:36,483] [INFO] Running command: hmmsearch --tblout GCF_031458295.1_ASM3145829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference/reference_markers.hmm GCF_031458295.1_ASM3145829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:36,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:36,965] [INFO] Found 6/6 markers.
[2024-01-24 13:46:37,040] [INFO] Query marker FASTA was written to GCF_031458295.1_ASM3145829v1_genomic.fna/markers.fasta
[2024-01-24 13:46:37,041] [INFO] Task started: Blastn
[2024-01-24 13:46:37,041] [INFO] Running command: blastn -query GCF_031458295.1_ASM3145829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference/reference_markers.fasta -out GCF_031458295.1_ASM3145829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:38,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:38,314] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:38,314] [INFO] Target genome list was writen to GCF_031458295.1_ASM3145829v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:38,324] [INFO] Task started: fastANI
[2024-01-24 13:46:38,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbe15ce9-7d38-4a60-ab29-7184cc4c11f4/GCF_031458295.1_ASM3145829v1_genomic.fna.gz --refList GCF_031458295.1_ASM3145829v1_genomic.fna/target_genomes.txt --output GCF_031458295.1_ASM3145829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:54,955] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:54,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:54,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:54,968] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:54,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:54,969] [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	85.7573	1279	1945	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	85.6307	1219	1945	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	85.418	1340	1945	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	85.4146	1293	1945	95	below_threshold
Glycomyces albidus	strain=NEAU-7082	GCA_009451885.1	2656774	2656774	type	True	85.3897	1299	1945	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	85.3647	1244	1945	95	below_threshold
Glycomyces buryatensis	strain=18	GCA_004912275.1	2570927	2570927	type	True	82.5949	1159	1945	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	76.3998	311	1945	95	below_threshold
Streptomyces filamentosus	strain=JCM 4122	GCA_014654895.1	67294	67294	type	True	76.3517	579	1945	95	below_threshold
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	76.1807	486	1945	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	76.1783	570	1945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:54,971] [INFO] DFAST Taxonomy check result was written to GCF_031458295.1_ASM3145829v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:54,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:54,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:54,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference/checkm_data
[2024-01-24 13:46:54,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:55,036] [INFO] Task started: CheckM
[2024-01-24 13:46:55,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458295.1_ASM3145829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458295.1_ASM3145829v1_genomic.fna/checkm_input GCF_031458295.1_ASM3145829v1_genomic.fna/checkm_result
[2024-01-24 13:47:47,744] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:47,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:47,772] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:47,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:47,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458295.1_ASM3145829v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:47,773] [INFO] Task started: Blastn
[2024-01-24 13:47:47,773] [INFO] Running command: blastn -query GCF_031458295.1_ASM3145829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60679e46-c01f-41ab-bd71-d38c72b23606/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458295.1_ASM3145829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:49,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:49,652] [INFO] Selected 14 target genomes.
[2024-01-24 13:47:49,652] [INFO] Target genome list was writen to GCF_031458295.1_ASM3145829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:49,687] [INFO] Task started: fastANI
[2024-01-24 13:47:49,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbe15ce9-7d38-4a60-ab29-7184cc4c11f4/GCF_031458295.1_ASM3145829v1_genomic.fna.gz --refList GCF_031458295.1_ASM3145829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458295.1_ASM3145829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:08,794] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:08,813] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:48:08,813] [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_017592475.1	s__Glycomyces sp017592475	89.6961	1478	1945	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	89.2797	1435	1945	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	85.787	1274	1945	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	85.7593	1335	1945	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	85.6536	1216	1945	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	85.4469	1290	1945	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	85.392	1343	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
GCF_004912155.1	s__Glycomyces paridis	85.3843	1242	1945	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	85.2005	1171	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004912275.1	s__Glycomyces buryatensis	82.5932	1159	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517975.1	s__Thermobifida cellulosilytica	76.3816	314	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863255.1	s__Planosporangium mesophilum	76.3767	437	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654895.1	s__Streptomyces filamentosus	76.3641	577	1945	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCA_002343325.1	s__UBA2396 sp002343325	74.7671	64	1945	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:08,815] [INFO] GTDB search result was written to GCF_031458295.1_ASM3145829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:08,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:08,820] [INFO] DFAST_QC result json was written to GCF_031458295.1_ASM3145829v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:08,820] [INFO] DFAST_QC completed!
[2024-01-24 13:48:08,820] [INFO] Total running time: 0h1m50s