[2024-01-24 11:35:23,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,533] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference
[2024-01-24 11:35:26,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,241] [INFO] Running command: gunzip -c /var/lib/cwl/stge0168a78-e3b4-42ab-b5d5-2bc10b7af51e/GCF_005930495.1_ASM593049v1_genomic.fna.gz | prodigal -d GCF_005930495.1_ASM593049v1_genomic.fna/cds.fna -a GCF_005930495.1_ASM593049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:39,694] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:39,694] [INFO] Task started: HMMsearch
[2024-01-24 11:35:39,694] [INFO] Running command: hmmsearch --tblout GCF_005930495.1_ASM593049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference/reference_markers.hmm GCF_005930495.1_ASM593049v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:40,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:40,050] [INFO] Found 6/6 markers.
[2024-01-24 11:35:40,093] [INFO] Query marker FASTA was written to GCF_005930495.1_ASM593049v1_genomic.fna/markers.fasta
[2024-01-24 11:35:40,094] [INFO] Task started: Blastn
[2024-01-24 11:35:40,094] [INFO] Running command: blastn -query GCF_005930495.1_ASM593049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference/reference_markers.fasta -out GCF_005930495.1_ASM593049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:41,357] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:41,360] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:41,361] [INFO] Target genome list was writen to GCF_005930495.1_ASM593049v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:41,365] [INFO] Task started: fastANI
[2024-01-24 11:35:41,365] [INFO] Running command: fastANI --query /var/lib/cwl/stge0168a78-e3b4-42ab-b5d5-2bc10b7af51e/GCF_005930495.1_ASM593049v1_genomic.fna.gz --refList GCF_005930495.1_ASM593049v1_genomic.fna/target_genomes.txt --output GCF_005930495.1_ASM593049v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:54,914] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:54,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:54,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:54,927] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:54,928] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:54,928] [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 excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	100.0	1659	1669	95	conclusive
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	92.7753	1302	1669	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	86.9478	1062	1669	95	below_threshold
Modestobacter versicolor	strain=CP153-2	GCA_003226595.1	429133	429133	type	True	86.9099	862	1669	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	84.8315	976	1669	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	84.7625	951	1669	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	84.4899	969	1669	95	below_threshold
Goekera deserti	strain=CPCC 205119	GCA_010685995.1	2497753	2497753	type	True	82.4026	905	1669	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	82.3358	934	1669	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.3026	932	1669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:54,930] [INFO] DFAST Taxonomy check result was written to GCF_005930495.1_ASM593049v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:54,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:54,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:54,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference/checkm_data
[2024-01-24 11:35:54,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:54,981] [INFO] Task started: CheckM
[2024-01-24 11:35:54,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005930495.1_ASM593049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005930495.1_ASM593049v1_genomic.fna/checkm_input GCF_005930495.1_ASM593049v1_genomic.fna/checkm_result
[2024-01-24 11:37:08,856] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:08,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:08,876] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:08,877] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:08,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005930495.1_ASM593049v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:08,877] [INFO] Task started: Blastn
[2024-01-24 11:37:08,877] [INFO] Running command: blastn -query GCF_005930495.1_ASM593049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf10dc52-d999-47fc-8f7f-94db966ac410/dqc_reference/reference_markers_gtdb.fasta -out GCF_005930495.1_ASM593049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:10,689] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:10,693] [INFO] Selected 9 target genomes.
[2024-01-24 11:37:10,694] [INFO] Target genome list was writen to GCF_005930495.1_ASM593049v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:10,701] [INFO] Task started: fastANI
[2024-01-24 11:37:10,701] [INFO] Running command: fastANI --query /var/lib/cwl/stge0168a78-e3b4-42ab-b5d5-2bc10b7af51e/GCF_005930495.1_ASM593049v1_genomic.fna.gz --refList GCF_005930495.1_ASM593049v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005930495.1_ASM593049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:23,979] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:23,993] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:23,994] [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_005930495.1	s__Modestobacter excelsi	100.0	1659	1669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005930475.1	s__Modestobacter altitudinis	92.8173	1299	1669	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	92.1575	1264	1669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	91.5277	1262	1669	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	86.9676	1062	1669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.97	99.97	1.00	1.00	2	-
GCF_011758655.1	s__Modestobacter marinus	85.2844	1036	1669	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	84.7683	950	1669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007994135.1	s__Modestobacter roseus	84.4692	971	1669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	99.87	99.87	0.97	0.97	2	-
GCF_900215145.1	s__Geodermatophilus sabuli	82.306	937	1669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:23,995] [INFO] GTDB search result was written to GCF_005930495.1_ASM593049v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:23,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:23,999] [INFO] DFAST_QC result json was written to GCF_005930495.1_ASM593049v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:23,999] [INFO] DFAST_QC completed!
[2024-01-24 11:37:23,999] [INFO] Total running time: 0h2m0s