[2024-01-25 19:56:05,670] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:05,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:05,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference
[2024-01-25 19:56:06,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:06,909] [INFO] Task started: Prodigal
[2024-01-25 19:56:06,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgc39615b7-802d-4a8b-a2ed-1bf1a665c982/GCF_002735305.1_ASM273530v1_genomic.fna.gz | prodigal -d GCF_002735305.1_ASM273530v1_genomic.fna/cds.fna -a GCF_002735305.1_ASM273530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:13,783] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:13,784] [INFO] Task started: HMMsearch
[2024-01-25 19:56:13,784] [INFO] Running command: hmmsearch --tblout GCF_002735305.1_ASM273530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference/reference_markers.hmm GCF_002735305.1_ASM273530v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:14,012] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:14,015] [INFO] Found 6/6 markers.
[2024-01-25 19:56:14,041] [INFO] Query marker FASTA was written to GCF_002735305.1_ASM273530v1_genomic.fna/markers.fasta
[2024-01-25 19:56:14,042] [INFO] Task started: Blastn
[2024-01-25 19:56:14,042] [INFO] Running command: blastn -query GCF_002735305.1_ASM273530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference/reference_markers.fasta -out GCF_002735305.1_ASM273530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:14,641] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:14,644] [INFO] Selected 28 target genomes.
[2024-01-25 19:56:14,644] [INFO] Target genome list was writen to GCF_002735305.1_ASM273530v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:14,665] [INFO] Task started: fastANI
[2024-01-25 19:56:14,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39615b7-802d-4a8b-a2ed-1bf1a665c982/GCF_002735305.1_ASM273530v1_genomic.fna.gz --refList GCF_002735305.1_ASM273530v1_genomic.fna/target_genomes.txt --output GCF_002735305.1_ASM273530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:30,089] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:30,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:30,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:30,096] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:30,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:30,096] [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
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	100.0	897	897	95	conclusive
Pseudobutyrivibrio ruminis	strain=DSM 9787	GCA_900218035.1	46206	46206	suspected-type	True	78.7603	55	897	95	below_threshold
Eubacterium oxidoreducens	strain=DSM 3217	GCA_900104415.1	1732	1732	type	True	78.39	61	897	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.978	81	897	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	77.8784	110	897	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.5054	78	897	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.4479	81	897	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.3734	79	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:30,098] [INFO] DFAST Taxonomy check result was written to GCF_002735305.1_ASM273530v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:30,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:30,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:30,099] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference/checkm_data
[2024-01-25 19:56:30,100] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:30,130] [INFO] Task started: CheckM
[2024-01-25 19:56:30,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002735305.1_ASM273530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002735305.1_ASM273530v1_genomic.fna/checkm_input GCF_002735305.1_ASM273530v1_genomic.fna/checkm_result
[2024-01-25 19:56:55,424] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:55,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:55,447] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:55,447] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:55,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002735305.1_ASM273530v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:55,447] [INFO] Task started: Blastn
[2024-01-25 19:56:55,447] [INFO] Running command: blastn -query GCF_002735305.1_ASM273530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9cad618-15fc-4979-84e2-6fb8792fdb42/dqc_reference/reference_markers_gtdb.fasta -out GCF_002735305.1_ASM273530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:56,471] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:56,474] [INFO] Selected 26 target genomes.
[2024-01-25 19:56:56,474] [INFO] Target genome list was writen to GCF_002735305.1_ASM273530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:56,509] [INFO] Task started: fastANI
[2024-01-25 19:56:56,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39615b7-802d-4a8b-a2ed-1bf1a665c982/GCF_002735305.1_ASM273530v1_genomic.fna.gz --refList GCF_002735305.1_ASM273530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002735305.1_ASM273530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:10,615] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:10,624] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:10,624] [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_002735305.1	s__Agathobacter ruminis	100.0	897	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.23	97.94	0.91	0.87	3	conclusive
GCA_015057085.1	s__Agathobacter sp015057085	82.5322	398	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317585.1	s__Agathobacter sp900317585	78.4218	83	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCF_000174195.1	s__Roseburia inulinivorans	77.978	81	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCF_001406815.1	s__Agathobacter faecis	77.8784	110	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCF_001940165.1	s__Roseburia sp001940165	77.4587	95	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409825.1	s__Agathobacter sp017409825	77.1423	56	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.24	96.24	0.85	0.85	2	-
GCA_900552085.1	s__Agathobacter sp900552085	77.0523	71	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_003483745.1	s__Roseburia sp003483745	77.0072	61	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_012519695.1	s__14-2 sp012519695	76.8842	50	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	97.81	97.81	0.86	0.86	2	-
GCA_900550545.1	s__Agathobacter sp900550545	76.6991	92	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900753715.1	s__Roseburia sp900753715	76.6593	67	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	99.04	99.04	0.83	0.83	2	-
GCA_910587655.1	s__Agathobacter sp910587655	76.3087	69	897	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:10,626] [INFO] GTDB search result was written to GCF_002735305.1_ASM273530v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:10,626] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:10,629] [INFO] DFAST_QC result json was written to GCF_002735305.1_ASM273530v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:10,629] [INFO] DFAST_QC completed!
[2024-01-25 19:57:10,629] [INFO] Total running time: 0h1m5s