[2024-01-24 13:24:48,086] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:24:48,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:24:48,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference
[2024-01-24 13:24:49,446] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:24:49,447] [INFO] Task started: Prodigal
[2024-01-24 13:24:49,447] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7d6895c-f071-4cda-91b3-1ff2b463cbf0/GCF_003254255.1_ASM325425v1_genomic.fna.gz | prodigal -d GCF_003254255.1_ASM325425v1_genomic.fna/cds.fna -a GCF_003254255.1_ASM325425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:24:54,962] [INFO] Task succeeded: Prodigal
[2024-01-24 13:24:54,962] [INFO] Task started: HMMsearch
[2024-01-24 13:24:54,963] [INFO] Running command: hmmsearch --tblout GCF_003254255.1_ASM325425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference/reference_markers.hmm GCF_003254255.1_ASM325425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:24:55,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:24:55,235] [INFO] Found 6/6 markers.
[2024-01-24 13:24:55,267] [INFO] Query marker FASTA was written to GCF_003254255.1_ASM325425v1_genomic.fna/markers.fasta
[2024-01-24 13:24:55,268] [INFO] Task started: Blastn
[2024-01-24 13:24:55,268] [INFO] Running command: blastn -query GCF_003254255.1_ASM325425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference/reference_markers.fasta -out GCF_003254255.1_ASM325425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:55,995] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:55,999] [INFO] Selected 11 target genomes.
[2024-01-24 13:24:56,000] [INFO] Target genome list was writen to GCF_003254255.1_ASM325425v1_genomic.fna/target_genomes.txt
[2024-01-24 13:24:56,034] [INFO] Task started: fastANI
[2024-01-24 13:24:56,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d6895c-f071-4cda-91b3-1ff2b463cbf0/GCF_003254255.1_ASM325425v1_genomic.fna.gz --refList GCF_003254255.1_ASM325425v1_genomic.fna/target_genomes.txt --output GCF_003254255.1_ASM325425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:03,020] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:03,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:03,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:03,032] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:03,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:03,032] [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 umeaense	strain=DSM 23576	GCA_003254255.1	617123	617123	type	True	99.9999	860	862	95	conclusive
Lachnoanaerobaculum umeaense	strain=DSM 23576 = CCUG 58757	GCA_003589745.1	617123	617123	type	True	99.9961	860	862	95	conclusive
Lachnoanaerobaculum gingivalis	strain=KCOM 2030	GCA_003862475.1	2490855	2490855	type	True	85.5927	607	862	95	below_threshold
Lachnoanaerobaculum orale	strain=DSM 24553	GCA_003862485.1	979627	979627	type	True	82.7823	561	862	95	below_threshold
Lachnoanaerobaculum saburreum	strain=DSM 3986	GCA_000185385.1	467210	467210	type	True	82.0095	538	862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:03,033] [INFO] DFAST Taxonomy check result was written to GCF_003254255.1_ASM325425v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:03,034] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:03,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:03,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference/checkm_data
[2024-01-24 13:25:03,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:03,063] [INFO] Task started: CheckM
[2024-01-24 13:25:03,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254255.1_ASM325425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254255.1_ASM325425v1_genomic.fna/checkm_input GCF_003254255.1_ASM325425v1_genomic.fna/checkm_result
[2024-01-24 13:25:26,070] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:26,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:26,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:26,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:26,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254255.1_ASM325425v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:26,089] [INFO] Task started: Blastn
[2024-01-24 13:25:26,089] [INFO] Running command: blastn -query GCF_003254255.1_ASM325425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f0ca72a-0201-4e36-afde-926a75bd5dfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254255.1_ASM325425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:27,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:27,082] [INFO] Selected 7 target genomes.
[2024-01-24 13:25:27,083] [INFO] Target genome list was writen to GCF_003254255.1_ASM325425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:27,101] [INFO] Task started: fastANI
[2024-01-24 13:25:27,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d6895c-f071-4cda-91b3-1ff2b463cbf0/GCF_003254255.1_ASM325425v1_genomic.fna.gz --refList GCF_003254255.1_ASM325425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254255.1_ASM325425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:32,020] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:32,033] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:32,033] [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_003589745.1	s__Lachnoanaerobaculum umeaense	99.9961	860	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000287675.1	s__Lachnoanaerobaculum sp000287675	86.2603	616	862	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	85.7207	611	862	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	85.5495	610	862	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	83.6503	599	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	98.01	98.01	0.91	0.91	2	-
GCF_003862485.1	s__Lachnoanaerobaculum orale	82.7844	561	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	95.98	95.69	0.85	0.82	6	-
GCF_000185385.1	s__Lachnoanaerobaculum saburreum	82.0084	538	862	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoanaerobaculum	95.0	97.52	97.46	0.88	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:32,034] [INFO] GTDB search result was written to GCF_003254255.1_ASM325425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:32,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:32,037] [INFO] DFAST_QC result json was written to GCF_003254255.1_ASM325425v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:32,038] [INFO] DFAST_QC completed!
[2024-01-24 13:25:32,038] [INFO] Total running time: 0h0m44s