[2024-01-24 15:26:38,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:38,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:38,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference
[2024-01-24 15:26:40,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,168] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg8af0bd5c-0b4c-4a09-b517-8f8f005bd5d8/GCF_014195485.1_ASM1419548v1_genomic.fna.gz | prodigal -d GCF_014195485.1_ASM1419548v1_genomic.fna/cds.fna -a GCF_014195485.1_ASM1419548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:52,545] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:52,546] [INFO] Task started: HMMsearch
[2024-01-24 15:26:52,546] [INFO] Running command: hmmsearch --tblout GCF_014195485.1_ASM1419548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference/reference_markers.hmm GCF_014195485.1_ASM1419548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:52,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:52,862] [INFO] Found 6/6 markers.
[2024-01-24 15:26:52,906] [INFO] Query marker FASTA was written to GCF_014195485.1_ASM1419548v1_genomic.fna/markers.fasta
[2024-01-24 15:26:52,906] [INFO] Task started: Blastn
[2024-01-24 15:26:52,906] [INFO] Running command: blastn -query GCF_014195485.1_ASM1419548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference/reference_markers.fasta -out GCF_014195485.1_ASM1419548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:54,249] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:54,253] [INFO] Selected 10 target genomes.
[2024-01-24 15:26:54,253] [INFO] Target genome list was writen to GCF_014195485.1_ASM1419548v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:54,258] [INFO] Task started: fastANI
[2024-01-24 15:26:54,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg8af0bd5c-0b4c-4a09-b517-8f8f005bd5d8/GCF_014195485.1_ASM1419548v1_genomic.fna.gz --refList GCF_014195485.1_ASM1419548v1_genomic.fna/target_genomes.txt --output GCF_014195485.1_ASM1419548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:10,102] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:10,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:10,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:10,112] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:10,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:10,112] [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 versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	100.0	1527	1530	95	conclusive
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	99.678	1176	1530	95	conclusive
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	87.3434	1047	1530	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	87.2737	1104	1530	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	86.2117	1088	1530	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	86.2089	1138	1530	95	below_threshold
Modestobacter marinus	strain=CGMCC 4.5581	GCA_014645755.1	477641	477641	type	True	86.1718	1121	1530	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	85.8897	1048	1530	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	85.8802	1015	1530	95	below_threshold
Goekera deserti	strain=CPCC 205119	GCA_010685995.1	2497753	2497753	type	True	82.9113	996	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:10,113] [INFO] DFAST Taxonomy check result was written to GCF_014195485.1_ASM1419548v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:10,114] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:10,114] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:10,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference/checkm_data
[2024-01-24 15:27:10,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:10,161] [INFO] Task started: CheckM
[2024-01-24 15:27:10,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195485.1_ASM1419548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195485.1_ASM1419548v1_genomic.fna/checkm_input GCF_014195485.1_ASM1419548v1_genomic.fna/checkm_result
[2024-01-24 15:28:24,261] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:24,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:24,286] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:24,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:24,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195485.1_ASM1419548v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:24,287] [INFO] Task started: Blastn
[2024-01-24 15:28:24,287] [INFO] Running command: blastn -query GCF_014195485.1_ASM1419548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7d84cf-a92e-4b8c-b018-145072beee39/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195485.1_ASM1419548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:26,274] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:26,283] [INFO] Selected 9 target genomes.
[2024-01-24 15:28:26,283] [INFO] Target genome list was writen to GCF_014195485.1_ASM1419548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:26,291] [INFO] Task started: fastANI
[2024-01-24 15:28:26,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg8af0bd5c-0b4c-4a09-b517-8f8f005bd5d8/GCF_014195485.1_ASM1419548v1_genomic.fna.gz --refList GCF_014195485.1_ASM1419548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195485.1_ASM1419548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:40,381] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:40,393] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:40,393] [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_014195485.1	s__Modestobacter versicolor	100.0	1525	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_000306785.1	s__Modestobacter marinus_A	87.5839	1193	1530	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	87.3471	1047	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930475.1	s__Modestobacter altitudinis	87.2345	1109	1530	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	87.0336	1157	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761485.1	s__Modestobacter caceresii	86.2783	1082	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	98.27	98.27	0.83	0.83	2	-
GCF_011758655.1	s__Modestobacter marinus	86.2666	1132	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010682105.1	s__Modestobacter muralis	85.8702	1016	1530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019112525.1	s__Modestobacter sp019112525	85.6699	1067	1530	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 15:28:40,400] [INFO] GTDB search result was written to GCF_014195485.1_ASM1419548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:40,401] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:40,406] [INFO] DFAST_QC result json was written to GCF_014195485.1_ASM1419548v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:40,407] [INFO] DFAST_QC completed!
[2024-01-24 15:28:40,407] [INFO] Total running time: 0h2m2s