[2024-01-24 13:28:17,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:17,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:17,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference
[2024-01-24 13:28:18,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:18,916] [INFO] Task started: Prodigal
[2024-01-24 13:28:18,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fb5138a-1f8b-4694-a166-33b5a3049a45/GCF_007828865.1_ASM782886v1_genomic.fna.gz | prodigal -d GCF_007828865.1_ASM782886v1_genomic.fna/cds.fna -a GCF_007828865.1_ASM782886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:42,034] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:42,034] [INFO] Task started: HMMsearch
[2024-01-24 13:28:42,034] [INFO] Running command: hmmsearch --tblout GCF_007828865.1_ASM782886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference/reference_markers.hmm GCF_007828865.1_ASM782886v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:42,527] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:42,529] [INFO] Found 6/6 markers.
[2024-01-24 13:28:42,606] [INFO] Query marker FASTA was written to GCF_007828865.1_ASM782886v1_genomic.fna/markers.fasta
[2024-01-24 13:28:42,606] [INFO] Task started: Blastn
[2024-01-24 13:28:42,607] [INFO] Running command: blastn -query GCF_007828865.1_ASM782886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference/reference_markers.fasta -out GCF_007828865.1_ASM782886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:43,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:43,977] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:43,978] [INFO] Target genome list was writen to GCF_007828865.1_ASM782886v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:43,990] [INFO] Task started: fastANI
[2024-01-24 13:28:43,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fb5138a-1f8b-4694-a166-33b5a3049a45/GCF_007828865.1_ASM782886v1_genomic.fna.gz --refList GCF_007828865.1_ASM782886v1_genomic.fna/target_genomes.txt --output GCF_007828865.1_ASM782886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:12,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:12,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:12,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:12,985] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:12,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:12,986] [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
Kribbella amoyensis	strain=DSM 24683	GCA_007828865.1	996641	996641	type	True	100.0	2703	2703	95	conclusive
Kribbella flavida	strain=DSM 17836	GCA_000024345.1	182640	182640	type	True	84.7022	1695	2703	95	below_threshold
Kribbella italica	strain=DSM 28967	GCA_014205135.1	1540520	1540520	type	True	84.2023	1832	2703	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	83.7747	1529	2703	95	below_threshold
Kribbella catacumbae	strain=DSM 19601	GCA_000372465.1	460086	460086	type	True	83.1837	1587	2703	95	below_threshold
Kribbella monticola	strain=NEAU-SW521	GCA_003261635.1	2185285	2185285	type	True	83.075	1574	2703	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	83.0369	1694	2703	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	82.9192	1689	2703	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	82.8775	1555	2703	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	82.8085	1506	2703	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	82.7816	1691	2703	95	below_threshold
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	82.6149	1710	2703	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	82.5351	1580	2703	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.812	624	2703	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:12,987] [INFO] DFAST Taxonomy check result was written to GCF_007828865.1_ASM782886v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:12,988] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:12,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:12,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference/checkm_data
[2024-01-24 13:29:12,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:13,070] [INFO] Task started: CheckM
[2024-01-24 13:29:13,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007828865.1_ASM782886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007828865.1_ASM782886v1_genomic.fna/checkm_input GCF_007828865.1_ASM782886v1_genomic.fna/checkm_result
[2024-01-24 13:30:45,946] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:45,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:45,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:45,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:45,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007828865.1_ASM782886v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:45,971] [INFO] Task started: Blastn
[2024-01-24 13:30:45,971] [INFO] Running command: blastn -query GCF_007828865.1_ASM782886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e5c7620-7600-4e58-b570-e7064279ea8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007828865.1_ASM782886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:48,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:48,142] [INFO] Selected 16 target genomes.
[2024-01-24 13:30:48,142] [INFO] Target genome list was writen to GCF_007828865.1_ASM782886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:48,162] [INFO] Task started: fastANI
[2024-01-24 13:30:48,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fb5138a-1f8b-4694-a166-33b5a3049a45/GCF_007828865.1_ASM782886v1_genomic.fna.gz --refList GCF_007828865.1_ASM782886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007828865.1_ASM782886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:20,050] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:20,070] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:20,071] [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_007828865.1	s__Kribbella amoyensis	100.0	2702	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000024345.1	s__Kribbella flavida	84.723	1692	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361855.1	s__Kribbella sp004361855	84.536	1766	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984195.1	s__Kribbella sp001984195	84.5069	1773	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205135.1	s__Kribbella italica	84.199	1833	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348725.1	s__Kribbella sp004348725	83.7782	1529	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342025.1	s__Kribbella sp004342025	83.3128	1718	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372465.1	s__Kribbella catacumbae	83.19	1586	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365175.1	s__Kribbella sp004365175	83.0906	1640	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261635.1	s__Kribbella monticola	83.0638	1576	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345665.1	s__Kribbella sp004345665	82.9999	1556	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	82.8617	1556	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331345.1	s__Kribbella soli	82.628	1708	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233875.1	s__Kribbella sp005233875	82.5265	1584	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365875.1	s__Kribbella sp004365875	82.494	1568	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217145.1	s__Kribbella soli_A	82.2519	1595	2703	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:20,072] [INFO] GTDB search result was written to GCF_007828865.1_ASM782886v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:20,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:20,077] [INFO] DFAST_QC result json was written to GCF_007828865.1_ASM782886v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:20,077] [INFO] DFAST_QC completed!
[2024-01-24 13:31:20,077] [INFO] Total running time: 0h3m2s