[2024-01-24 15:18:37,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:37,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:37,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference
[2024-01-24 15:18:39,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,189] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,189] [INFO] Running command: gunzip -c /var/lib/cwl/stgb52fdd75-3e41-4ed8-a489-875fb50d575a/GCF_003724155.1_ASM372415v1_genomic.fna.gz | prodigal -d GCF_003724155.1_ASM372415v1_genomic.fna/cds.fna -a GCF_003724155.1_ASM372415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:52,823] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:52,824] [INFO] Task started: HMMsearch
[2024-01-24 15:18:52,824] [INFO] Running command: hmmsearch --tblout GCF_003724155.1_ASM372415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference/reference_markers.hmm GCF_003724155.1_ASM372415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:53,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:53,168] [INFO] Found 6/6 markers.
[2024-01-24 15:18:53,211] [INFO] Query marker FASTA was written to GCF_003724155.1_ASM372415v1_genomic.fna/markers.fasta
[2024-01-24 15:18:53,211] [INFO] Task started: Blastn
[2024-01-24 15:18:53,211] [INFO] Running command: blastn -query GCF_003724155.1_ASM372415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference/reference_markers.fasta -out GCF_003724155.1_ASM372415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:54,471] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:54,474] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:54,474] [INFO] Target genome list was writen to GCF_003724155.1_ASM372415v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:54,480] [INFO] Task started: fastANI
[2024-01-24 15:18:54,480] [INFO] Running command: fastANI --query /var/lib/cwl/stgb52fdd75-3e41-4ed8-a489-875fb50d575a/GCF_003724155.1_ASM372415v1_genomic.fna.gz --refList GCF_003724155.1_ASM372415v1_genomic.fna/target_genomes.txt --output GCF_003724155.1_ASM372415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:07,208] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:07,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:07,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:07,221] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:07,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:07,221] [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
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	100.0	1356	1357	95	conclusive
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	82.6397	888	1357	95	below_threshold
Flexivirga endophytica	strain=KCTC 39536	GCA_014652735.1	1849103	1849103	type	True	81.9107	846	1357	95	below_threshold
Flexivirga endophytica	strain=CGMCC 1.15085	GCA_014640635.1	1849103	1849103	type	True	81.901	850	1357	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	81.2794	716	1357	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.2849	438	1357	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.0731	284	1357	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.0151	274	1357	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	77.9988	320	1357	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	77.9805	292	1357	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	77.8706	294	1357	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	77.7573	262	1357	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.4417	197	1357	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	76.4418	333	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:07,223] [INFO] DFAST Taxonomy check result was written to GCF_003724155.1_ASM372415v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:07,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:07,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:07,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference/checkm_data
[2024-01-24 15:19:07,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:07,269] [INFO] Task started: CheckM
[2024-01-24 15:19:07,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003724155.1_ASM372415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003724155.1_ASM372415v1_genomic.fna/checkm_input GCF_003724155.1_ASM372415v1_genomic.fna/checkm_result
[2024-01-24 15:19:52,775] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:52,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:52,799] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:52,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:52,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003724155.1_ASM372415v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:52,800] [INFO] Task started: Blastn
[2024-01-24 15:19:52,800] [INFO] Running command: blastn -query GCF_003724155.1_ASM372415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86b299c5-c9f1-44b1-a942-69776a8a4453/dqc_reference/reference_markers_gtdb.fasta -out GCF_003724155.1_ASM372415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:54,693] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:54,697] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:54,697] [INFO] Target genome list was writen to GCF_003724155.1_ASM372415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:54,708] [INFO] Task started: fastANI
[2024-01-24 15:19:54,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgb52fdd75-3e41-4ed8-a489-875fb50d575a/GCF_003724155.1_ASM372415v1_genomic.fna.gz --refList GCF_003724155.1_ASM372415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003724155.1_ASM372415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:04,827] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:04,848] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:04,849] [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_003724155.1	s__Flexivirga caeni	100.0	1356	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014190805.1	s__Flexivirga oryzae	82.6052	893	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640635.1	s__Flexivirga endophytica	81.8872	852	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013002715.1	s__Flexivirga aerilata	81.3045	713	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829035.1	s__Rudaeicoccus suwonensis	79.5716	547	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Rudaeicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013135345.1	s__Yimella sp013135345	79.3996	455	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001247745.1	s__Luteipulveratus halotolerans	79.2849	438	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017565405.1	s__Allobranchiibius sp017565405	78.7343	451	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001594145.1	s__Branchiibius sp001594145	78.606	375	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Branchiibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.4596	370	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	77.9998	320	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	77.9621	373	1357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:04,851] [INFO] GTDB search result was written to GCF_003724155.1_ASM372415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:04,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:04,858] [INFO] DFAST_QC result json was written to GCF_003724155.1_ASM372415v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:04,858] [INFO] DFAST_QC completed!
[2024-01-24 15:20:04,858] [INFO] Total running time: 0h1m27s