[2024-01-24 12:22:37,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:37,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:37,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference
[2024-01-24 12:22:39,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,302] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,302] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8a35ffb-65d1-49a4-b0d3-470231b03876/GCF_010686625.1_ASM1068662v1_genomic.fna.gz | prodigal -d GCF_010686625.1_ASM1068662v1_genomic.fna/cds.fna -a GCF_010686625.1_ASM1068662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:51,348] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:51,349] [INFO] Task started: HMMsearch
[2024-01-24 12:22:51,349] [INFO] Running command: hmmsearch --tblout GCF_010686625.1_ASM1068662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference/reference_markers.hmm GCF_010686625.1_ASM1068662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:51,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:51,631] [INFO] Found 6/6 markers.
[2024-01-24 12:22:51,690] [INFO] Query marker FASTA was written to GCF_010686625.1_ASM1068662v1_genomic.fna/markers.fasta
[2024-01-24 12:22:51,690] [INFO] Task started: Blastn
[2024-01-24 12:22:51,691] [INFO] Running command: blastn -query GCF_010686625.1_ASM1068662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference/reference_markers.fasta -out GCF_010686625.1_ASM1068662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:52,972] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:52,975] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:52,975] [INFO] Target genome list was writen to GCF_010686625.1_ASM1068662v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:52,981] [INFO] Task started: fastANI
[2024-01-24 12:22:52,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8a35ffb-65d1-49a4-b0d3-470231b03876/GCF_010686625.1_ASM1068662v1_genomic.fna.gz --refList GCF_010686625.1_ASM1068662v1_genomic.fna/target_genomes.txt --output GCF_010686625.1_ASM1068662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:06,114] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:06,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:06,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:06,131] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:06,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:06,132] [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
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	100.0	1422	1474	95	conclusive
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	100.0	1473	1474	95	conclusive
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	85.9313	860	1474	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	85.8594	1044	1474	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	85.0468	1022	1474	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	85.0009	966	1474	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	84.9649	1037	1474	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	84.9231	1019	1474	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	84.9174	965	1474	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	84.6644	991	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,134] [INFO] DFAST Taxonomy check result was written to GCF_010686625.1_ASM1068662v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:06,134] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:06,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:06,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference/checkm_data
[2024-01-24 12:23:06,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:06,183] [INFO] Task started: CheckM
[2024-01-24 12:23:06,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010686625.1_ASM1068662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010686625.1_ASM1068662v1_genomic.fna/checkm_input GCF_010686625.1_ASM1068662v1_genomic.fna/checkm_result
[2024-01-24 12:24:14,251] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:14,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:14,280] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:14,281] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:14,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010686625.1_ASM1068662v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:14,282] [INFO] Task started: Blastn
[2024-01-24 12:24:14,282] [INFO] Running command: blastn -query GCF_010686625.1_ASM1068662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg444f72d2-5d5f-412e-8b34-3654a9695c74/dqc_reference/reference_markers_gtdb.fasta -out GCF_010686625.1_ASM1068662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:16,235] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:16,238] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:16,239] [INFO] Target genome list was writen to GCF_010686625.1_ASM1068662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:16,249] [INFO] Task started: fastANI
[2024-01-24 12:24:16,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8a35ffb-65d1-49a4-b0d3-470231b03876/GCF_010686625.1_ASM1068662v1_genomic.fna.gz --refList GCF_010686625.1_ASM1068662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010686625.1_ASM1068662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:31,555] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:31,570] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:31,570] [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_010682105.1	s__Modestobacter muralis	100.0	1422	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_019112525.1	s__Modestobacter sp019112525	90.369	1132	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195485.1	s__Modestobacter versicolor	85.8998	1040	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000306785.1	s__Modestobacter marinus_A	85.4253	1080	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758655.1	s__Modestobacter marinus	85.05	1021	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000761485.1	s__Modestobacter caceresii	85.0241	964	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	98.27	98.27	0.83	0.83	2	-
GCF_005930475.1	s__Modestobacter altitudinis	84.9899	1012	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620205.1	s__Modestobacter sp000620205	84.9828	1020	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930495.1	s__Modestobacter excelsi	84.9175	965	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994135.1	s__Modestobacter roseus	84.7056	986	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_013408865.1	s__Modestobacter sp013408865	83.0991	914	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:31,572] [INFO] GTDB search result was written to GCF_010686625.1_ASM1068662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:31,573] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:31,576] [INFO] DFAST_QC result json was written to GCF_010686625.1_ASM1068662v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:31,576] [INFO] DFAST_QC completed!
[2024-01-24 12:24:31,577] [INFO] Total running time: 0h1m54s