[2024-01-24 11:26:26,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:26,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:26,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference
[2024-01-24 11:26:27,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:27,696] [INFO] Task started: Prodigal
[2024-01-24 11:26:27,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgf551651f-34c1-4a06-beb5-4e83dd24cc53/GCF_016758255.1_ASM1675825v1_genomic.fna.gz | prodigal -d GCF_016758255.1_ASM1675825v1_genomic.fna/cds.fna -a GCF_016758255.1_ASM1675825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:37,786] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:37,787] [INFO] Task started: HMMsearch
[2024-01-24 11:26:37,787] [INFO] Running command: hmmsearch --tblout GCF_016758255.1_ASM1675825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference/reference_markers.hmm GCF_016758255.1_ASM1675825v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:38,069] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:38,070] [INFO] Found 6/6 markers.
[2024-01-24 11:26:38,100] [INFO] Query marker FASTA was written to GCF_016758255.1_ASM1675825v1_genomic.fna/markers.fasta
[2024-01-24 11:26:38,100] [INFO] Task started: Blastn
[2024-01-24 11:26:38,100] [INFO] Running command: blastn -query GCF_016758255.1_ASM1675825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference/reference_markers.fasta -out GCF_016758255.1_ASM1675825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:39,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:39,028] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:39,028] [INFO] Target genome list was writen to GCF_016758255.1_ASM1675825v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:39,032] [INFO] Task started: fastANI
[2024-01-24 11:26:39,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgf551651f-34c1-4a06-beb5-4e83dd24cc53/GCF_016758255.1_ASM1675825v1_genomic.fna.gz --refList GCF_016758255.1_ASM1675825v1_genomic.fna/target_genomes.txt --output GCF_016758255.1_ASM1675825v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:50,258] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:50,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:50,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:50,273] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:50,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:50,273] [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
Leucobacter luti	strain=RF6	GCA_004217175.1	340320	340320	suspected-type	True	82.2328	648	1071	95	below_threshold
Leucobacter luti	strain=RF6	GCA_016758235.1	340320	340320	suspected-type	True	82.1595	644	1071	95	below_threshold
Leucobacter chironomi	strain=DSM 19883	GCA_000421845.1	491918	491918	type	True	80.8522	502	1071	95	below_threshold
Leucobacter muris	strain=DSM 101948	GCA_004028235.1	1935379	1935379	type	True	80.7937	530	1071	95	below_threshold
Leucobacter ruminantium	strain=A2	GCA_017565705.1	1289170	1289170	type	True	80.6216	461	1071	95	below_threshold
Leucobacter celer subsp. astrifaciens	strain=CBX151	GCA_001273835.1	1461260	668625	type	True	80.4668	527	1071	95	below_threshold
Leucobacter zeae	strain=CC-MF41	GCA_016758175.1	1257004	1257004	type	True	80.4196	504	1071	95	below_threshold
Leucobacter triazinivorans	strain=JW-1	GCA_004208635.1	1784719	1784719	type	True	80.2384	505	1071	95	below_threshold
Leucobacter massiliensis	strain=122RC15	GCA_002982315.1	1686285	1686285	type	True	80.1516	447	1071	95	below_threshold
Leucobacter musarum subsp. musarum	strain=CBX152	GCA_001273845.1	1461261	1930747	type	True	79.9491	415	1071	95	below_threshold
Leucobacter japonicus	strain=CBX130	GCA_001273855.1	1461259	1461259	type	True	79.9148	461	1071	95	below_threshold
Leucobacter komagatae	strain=DSM 8803	GCA_006716085.1	55969	55969	type	True	79.8906	447	1071	95	below_threshold
Leucobacter salsicius	strain=M1-8	GCA_000350525.1	664638	664638	type	True	79.4699	405	1071	95	below_threshold
Leucobacter soli	strain=CIP 111803	GCA_910593785.1	2812850	2812850	type	True	79.3625	369	1071	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	77.6105	203	1071	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	77.5246	175	1071	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	77.4633	178	1071	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	76.9124	188	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:50,276] [INFO] DFAST Taxonomy check result was written to GCF_016758255.1_ASM1675825v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:50,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:50,276] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:50,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference/checkm_data
[2024-01-24 11:26:50,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:50,316] [INFO] Task started: CheckM
[2024-01-24 11:26:50,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016758255.1_ASM1675825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016758255.1_ASM1675825v1_genomic.fna/checkm_input GCF_016758255.1_ASM1675825v1_genomic.fna/checkm_result
[2024-01-24 11:27:25,982] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:25,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:26,005] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:26,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:26,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016758255.1_ASM1675825v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:26,006] [INFO] Task started: Blastn
[2024-01-24 11:27:26,006] [INFO] Running command: blastn -query GCF_016758255.1_ASM1675825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a21c7aa-6d3e-4420-9a73-b00a4186c00d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016758255.1_ASM1675825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:27,313] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:27,316] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:27,316] [INFO] Target genome list was writen to GCF_016758255.1_ASM1675825v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:27,327] [INFO] Task started: fastANI
[2024-01-24 11:27:27,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgf551651f-34c1-4a06-beb5-4e83dd24cc53/GCF_016758255.1_ASM1675825v1_genomic.fna.gz --refList GCF_016758255.1_ASM1675825v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016758255.1_ASM1675825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:34,829] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:34,843] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:34,843] [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_016758255.1	s__Leucobacter chromiireducens	100.0	1071	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003917135.1	s__Leucobacter chromiireducens_A	85.1681	782	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633415.1	s__Leucobacter sp000633415	84.8489	776	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217175.1	s__Leucobacter luti	82.2207	649	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016758195.1	s__Leucobacter solipictus	81.6398	599	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028235.1	s__Leucobacter muris	80.7639	533	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.77	98.77	0.90	0.90	2	-
GCF_016522535.1	s__Leucobacter sp016522535	80.5939	444	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016758175.1	s__Leucobacter zeae	80.4081	505	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339635.1	s__Leucobacter luti_A	80.0856	477	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	98.22	98.22	0.92	0.92	2	-
GCF_000350525.1	s__Leucobacter salsicius	79.4845	403	1071	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Leucobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,845] [INFO] GTDB search result was written to GCF_016758255.1_ASM1675825v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:34,846] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:34,850] [INFO] DFAST_QC result json was written to GCF_016758255.1_ASM1675825v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:34,850] [INFO] DFAST_QC completed!
[2024-01-24 11:27:34,850] [INFO] Total running time: 0h1m8s