[2024-01-24 14:47:08,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,398] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference
[2024-01-24 14:47:09,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,794] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg5273f3f1-5bb1-4aeb-94e6-313c778a2cfe/GCF_001657475.1_ASM165747v1_genomic.fna.gz | prodigal -d GCF_001657475.1_ASM165747v1_genomic.fna/cds.fna -a GCF_001657475.1_ASM165747v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:21,418] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:21,419] [INFO] Task started: HMMsearch
[2024-01-24 14:47:21,419] [INFO] Running command: hmmsearch --tblout GCF_001657475.1_ASM165747v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference/reference_markers.hmm GCF_001657475.1_ASM165747v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:21,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:21,702] [INFO] Found 6/6 markers.
[2024-01-24 14:47:21,740] [INFO] Query marker FASTA was written to GCF_001657475.1_ASM165747v1_genomic.fna/markers.fasta
[2024-01-24 14:47:21,740] [INFO] Task started: Blastn
[2024-01-24 14:47:21,740] [INFO] Running command: blastn -query GCF_001657475.1_ASM165747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference/reference_markers.fasta -out GCF_001657475.1_ASM165747v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:22,474] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:22,477] [INFO] Selected 19 target genomes.
[2024-01-24 14:47:22,477] [INFO] Target genome list was writen to GCF_001657475.1_ASM165747v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:22,498] [INFO] Task started: fastANI
[2024-01-24 14:47:22,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg5273f3f1-5bb1-4aeb-94e6-313c778a2cfe/GCF_001657475.1_ASM165747v1_genomic.fna.gz --refList GCF_001657475.1_ASM165747v1_genomic.fna/target_genomes.txt --output GCF_001657475.1_ASM165747v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:34,362] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:34,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:34,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:34,372] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:34,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:34,373] [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
Enteractinococcus helveticum	strain=UASWS1574	GCA_001657475.1	1837282	1837282	type	True	100.0	1178	1183	95	conclusive
Enteractinococcus coprophilus	strain=DSM 24083	GCA_006716305.1	1027633	1027633	type	True	83.3266	703	1183	95	below_threshold
Auritidibacter ignavus	strain=IMMIB L-1656	GCA_003703835.1	678932	678932	type	True	77.6999	80	1183	95	below_threshold
Auritidibacter ignavus	strain=DSM 45359	GCA_011758685.1	678932	678932	type	True	77.2493	81	1183	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	76.1776	58	1183	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	76.0721	52	1183	95	below_threshold
Arthrobacter crystallopoietes	strain=DSM 20117	GCA_002849715.1	37928	37928	type	True	76.0521	60	1183	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	75.9968	58	1183	95	below_threshold
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	75.8791	54	1183	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:34,375] [INFO] DFAST Taxonomy check result was written to GCF_001657475.1_ASM165747v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:34,375] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:34,375] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:34,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference/checkm_data
[2024-01-24 14:47:34,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:34,420] [INFO] Task started: CheckM
[2024-01-24 14:47:34,420] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001657475.1_ASM165747v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001657475.1_ASM165747v1_genomic.fna/checkm_input GCF_001657475.1_ASM165747v1_genomic.fna/checkm_result
[2024-01-24 14:48:12,789] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:12,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:12,809] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:12,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:12,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001657475.1_ASM165747v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:12,810] [INFO] Task started: Blastn
[2024-01-24 14:48:12,810] [INFO] Running command: blastn -query GCF_001657475.1_ASM165747v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0ea49a2-8e42-4aff-a86a-4d6b24d169f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001657475.1_ASM165747v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:13,986] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:13,990] [INFO] Selected 13 target genomes.
[2024-01-24 14:48:13,991] [INFO] Target genome list was writen to GCF_001657475.1_ASM165747v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:14,013] [INFO] Task started: fastANI
[2024-01-24 14:48:14,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg5273f3f1-5bb1-4aeb-94e6-313c778a2cfe/GCF_001657475.1_ASM165747v1_genomic.fna.gz --refList GCF_001657475.1_ASM165747v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001657475.1_ASM165747v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:21,449] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:21,467] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:21,467] [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_001657475.1	s__Enteractinococcus helveticum	100.0	1178	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Enteractinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006716305.1	s__Enteractinococcus coprophilus	83.3266	700	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Enteractinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115865.1	s__Yaniella excrementavium	78.8942	238	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Yaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420805.1	s__Yaniella halotolerans	78.7151	311	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Yaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113675.1	s__Yaniella excrementigallinarum	78.5434	198	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Yaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013393415.1	s__Yaniella sp013393415	78.5158	319	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Yaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002358975.1	s__Yaniella sp002358975	78.0244	205	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Yaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003703835.1	s__Auritidibacter ignavus	77.6999	80	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Auritidibacter	95.0	98.68	97.17	0.91	0.81	7	-
GCF_005877055.1	s__Citricoccus sp005877055	76.2717	68	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116905.1	s__Citricoccus terreus	76.0414	57	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422645.1	s__Arthrobacter_I sp001422645	75.7932	50	1183	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:21,469] [INFO] GTDB search result was written to GCF_001657475.1_ASM165747v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:21,469] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:21,473] [INFO] DFAST_QC result json was written to GCF_001657475.1_ASM165747v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:21,473] [INFO] DFAST_QC completed!
[2024-01-24 14:48:21,473] [INFO] Total running time: 0h1m13s