[2024-01-25 19:35:51,080] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference
[2024-01-25 19:35:52,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,297] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg69ba9438-6a32-465b-ba74-0a43e4b3203e/GCF_003862485.1_ASM386248v1_genomic.fna.gz | prodigal -d GCF_003862485.1_ASM386248v1_genomic.fna/cds.fna -a GCF_003862485.1_ASM386248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:57,717] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:57,717] [INFO] Task started: HMMsearch
[2024-01-25 19:35:57,718] [INFO] Running command: hmmsearch --tblout GCF_003862485.1_ASM386248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference/reference_markers.hmm GCF_003862485.1_ASM386248v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:57,997] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:57,998] [INFO] Found 6/6 markers.
[2024-01-25 19:35:58,023] [INFO] Query marker FASTA was written to GCF_003862485.1_ASM386248v1_genomic.fna/markers.fasta
[2024-01-25 19:35:58,023] [INFO] Task started: Blastn
[2024-01-25 19:35:58,023] [INFO] Running command: blastn -query GCF_003862485.1_ASM386248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference/reference_markers.fasta -out GCF_003862485.1_ASM386248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:58,605] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:58,607] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:58,608] [INFO] Target genome list was writen to GCF_003862485.1_ASM386248v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:58,616] [INFO] Task started: fastANI
[2024-01-25 19:35:58,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg69ba9438-6a32-465b-ba74-0a43e4b3203e/GCF_003862485.1_ASM386248v1_genomic.fna.gz --refList GCF_003862485.1_ASM386248v1_genomic.fna/target_genomes.txt --output GCF_003862485.1_ASM386248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:06,352] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:06,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:06,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:06,358] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:06,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:06,358] [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
Lachnoanaerobaculum orale	strain=DSM 24553	GCA_003862485.1	979627	979627	type	True	100.0	925	925	95	conclusive
Lachnoanaerobaculum saburreum	strain=DSM 3986	GCA_000185385.1	467210	467210	type	True	86.7786	696	925	95	below_threshold
Lachnoanaerobaculum gingivalis	strain=KCOM 2030	GCA_003862475.1	2490855	2490855	type	True	84.7333	665	925	95	below_threshold
Lachnoanaerobaculum umeaense	strain=DSM 23576 = CCUG 58757	GCA_003589745.1	617123	617123	type	True	83.0448	574	925	95	below_threshold
Lachnoanaerobaculum umeaense	strain=DSM 23576	GCA_003254255.1	617123	617123	type	True	82.8845	544	925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:06,360] [INFO] DFAST Taxonomy check result was written to GCF_003862485.1_ASM386248v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:06,360] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:06,360] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:06,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference/checkm_data
[2024-01-25 19:36:06,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:06,393] [INFO] Task started: CheckM
[2024-01-25 19:36:06,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003862485.1_ASM386248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003862485.1_ASM386248v1_genomic.fna/checkm_input GCF_003862485.1_ASM386248v1_genomic.fna/checkm_result
[2024-01-25 19:36:27,090] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:27,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:27,109] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:27,109] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:27,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003862485.1_ASM386248v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:27,110] [INFO] Task started: Blastn
[2024-01-25 19:36:27,110] [INFO] Running command: blastn -query GCF_003862485.1_ASM386248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c7d64ab-2dce-488a-9448-3630287b1428/dqc_reference/reference_markers_gtdb.fasta -out GCF_003862485.1_ASM386248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:28,059] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:28,062] [INFO] Selected 6 target genomes.
[2024-01-25 19:36:28,062] [INFO] Target genome list was writen to GCF_003862485.1_ASM386248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:28,066] [INFO] Task started: fastANI
[2024-01-25 19:36:28,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg69ba9438-6a32-465b-ba74-0a43e4b3203e/GCF_003862485.1_ASM386248v1_genomic.fna.gz --refList GCF_003862485.1_ASM386248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003862485.1_ASM386248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:32,325] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:32,330] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:32,330] [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_003862485.1	s__Lachnoanaerobaculum orale	100.0	925	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	95.98	95.69	0.85	0.82	6	conclusive
GCF_000185385.1	s__Lachnoanaerobaculum saburreum	86.7609	697	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	97.52	97.46	0.88	0.85	3	-
GCF_000287675.1	s__Lachnoanaerobaculum sp000287675	85.0577	661	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.71	96.71	0.86	0.86	2	-
GCF_000296385.1	s__Lachnoanaerobaculum sp000296385	84.9903	645	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	96.95	96.95	0.89	0.89	2	-
GCF_003862475.1	s__Lachnoanaerobaculum gingivalis	84.7513	665	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000209465.1	s__Lachnoanaerobaculum sp000209465	82.5496	593	925	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	98.01	98.01	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:32,332] [INFO] GTDB search result was written to GCF_003862485.1_ASM386248v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:32,332] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:32,335] [INFO] DFAST_QC result json was written to GCF_003862485.1_ASM386248v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:32,335] [INFO] DFAST_QC completed!
[2024-01-25 19:36:32,335] [INFO] Total running time: 0h0m41s