[2024-01-25 18:10:50,490] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:50,492] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:50,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference
[2024-01-25 18:10:51,581] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:51,584] [INFO] Task started: Prodigal
[2024-01-25 18:10:51,584] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3454f77-a1a5-48b2-a5e0-03e060a72463/GCF_024498295.1_ASM2449829v1_genomic.fna.gz | prodigal -d GCF_024498295.1_ASM2449829v1_genomic.fna/cds.fna -a GCF_024498295.1_ASM2449829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:56,412] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:56,413] [INFO] Task started: HMMsearch
[2024-01-25 18:10:56,413] [INFO] Running command: hmmsearch --tblout GCF_024498295.1_ASM2449829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference/reference_markers.hmm GCF_024498295.1_ASM2449829v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:56,608] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:56,609] [INFO] Found 6/6 markers.
[2024-01-25 18:10:56,627] [INFO] Query marker FASTA was written to GCF_024498295.1_ASM2449829v1_genomic.fna/markers.fasta
[2024-01-25 18:10:56,627] [INFO] Task started: Blastn
[2024-01-25 18:10:56,627] [INFO] Running command: blastn -query GCF_024498295.1_ASM2449829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference/reference_markers.fasta -out GCF_024498295.1_ASM2449829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:57,223] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:57,226] [INFO] Selected 22 target genomes.
[2024-01-25 18:10:57,227] [INFO] Target genome list was writen to GCF_024498295.1_ASM2449829v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:57,242] [INFO] Task started: fastANI
[2024-01-25 18:10:57,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3454f77-a1a5-48b2-a5e0-03e060a72463/GCF_024498295.1_ASM2449829v1_genomic.fna.gz --refList GCF_024498295.1_ASM2449829v1_genomic.fna/target_genomes.txt --output GCF_024498295.1_ASM2449829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:08,535] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:08,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:08,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:08,540] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:08,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:08,540] [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
Caproiciproducens galactitolivorans	strain=BS-1	GCA_004768785.1	642589	642589	type	True	77.7412	78	653	95	below_threshold
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	77.4426	94	653	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.0782	59	653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:08,541] [INFO] DFAST Taxonomy check result was written to GCF_024498295.1_ASM2449829v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:08,542] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:08,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:08,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference/checkm_data
[2024-01-25 18:11:08,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:08,565] [INFO] Task started: CheckM
[2024-01-25 18:11:08,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498295.1_ASM2449829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498295.1_ASM2449829v1_genomic.fna/checkm_input GCF_024498295.1_ASM2449829v1_genomic.fna/checkm_result
[2024-01-25 18:11:28,320] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:28,321] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:28,339] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:28,340] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:28,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498295.1_ASM2449829v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:28,340] [INFO] Task started: Blastn
[2024-01-25 18:11:28,340] [INFO] Running command: blastn -query GCF_024498295.1_ASM2449829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e02b361-2b67-4124-a3d7-e1e170e13078/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498295.1_ASM2449829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:29,402] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:29,405] [INFO] Selected 25 target genomes.
[2024-01-25 18:11:29,405] [INFO] Target genome list was writen to GCF_024498295.1_ASM2449829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:29,459] [INFO] Task started: fastANI
[2024-01-25 18:11:29,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3454f77-a1a5-48b2-a5e0-03e060a72463/GCF_024498295.1_ASM2449829v1_genomic.fna.gz --refList GCF_024498295.1_ASM2449829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498295.1_ASM2449829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:39,823] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:39,832] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:11:39,832] [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
GCA_900184925.1	s__Caproicibacter sp900184925	78.491	274	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004768785.1	s__Caproiciproducens galactitolivorans	77.7307	75	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002159845.1	s__Anaeromassilibacillus stercoravium	77.5743	62	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	98.79	98.27	0.94	0.87	13	-
GCF_004103755.1	s__Caproicibacter sp004103755	77.5534	101	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517675.1	s__Caproiciproducens sp012517675	77.5409	67	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012516295.1	s__Caproiciproducens sp012516295	77.4543	59	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009746625.1	s__Caproicibacter fermentans	77.4426	94	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	98.75	98.55	0.84	0.84	3	-
GCA_000752215.1	s__Caproiciproducens sp000752215	77.4018	77	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	98.70	97.09	0.94	0.88	5	-
GCA_002407675.1	s__Caproicibacter sp002407675	76.9122	75	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	99.19	98.45	0.83	0.65	19	-
GCA_002397355.1	s__Caproicibacter sp002397355	76.8764	80	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002409675.1	s__Caproicibacter sp002409675	76.7225	81	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	99.08	98.54	0.84	0.78	11	-
GCA_002316805.1	s__Caproicibacter sp002316805	76.7144	57	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	98.72	98.62	0.79	0.75	3	-
GCA_900546895.1	s__Caproiciproducens sp900546895	76.5505	58	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002411365.1	s__Caproicibacter sp002411365	76.2077	66	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	99.82	99.77	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:39,834] [INFO] GTDB search result was written to GCF_024498295.1_ASM2449829v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:39,834] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:39,837] [INFO] DFAST_QC result json was written to GCF_024498295.1_ASM2449829v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:39,837] [INFO] DFAST_QC completed!
[2024-01-25 18:11:39,837] [INFO] Total running time: 0h0m49s