[2024-01-24 14:19:15,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:15,651] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:15,651] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference
[2024-01-24 14:19:18,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:18,320] [INFO] Task started: Prodigal
[2024-01-24 14:19:18,320] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdc1987e-9847-4802-a142-228dc7f8aba5/GCF_000145035.1_ASM14503v1_genomic.fna.gz | prodigal -d GCF_000145035.1_ASM14503v1_genomic.fna/cds.fna -a GCF_000145035.1_ASM14503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:28,710] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:28,711] [INFO] Task started: HMMsearch
[2024-01-24 14:19:28,711] [INFO] Running command: hmmsearch --tblout GCF_000145035.1_ASM14503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference/reference_markers.hmm GCF_000145035.1_ASM14503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:29,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:29,109] [INFO] Found 6/6 markers.
[2024-01-24 14:19:29,148] [INFO] Query marker FASTA was written to GCF_000145035.1_ASM14503v1_genomic.fna/markers.fasta
[2024-01-24 14:19:29,149] [INFO] Task started: Blastn
[2024-01-24 14:19:29,149] [INFO] Running command: blastn -query GCF_000145035.1_ASM14503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference/reference_markers.fasta -out GCF_000145035.1_ASM14503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:30,051] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:30,055] [INFO] Selected 25 target genomes.
[2024-01-24 14:19:30,056] [INFO] Target genome list was writen to GCF_000145035.1_ASM14503v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:30,068] [INFO] Task started: fastANI
[2024-01-24 14:19:30,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdc1987e-9847-4802-a142-228dc7f8aba5/GCF_000145035.1_ASM14503v1_genomic.fna.gz --refList GCF_000145035.1_ASM14503v1_genomic.fna/target_genomes.txt --output GCF_000145035.1_ASM14503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:46,408] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:46,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:46,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:46,451] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:46,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:46,451] [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
Butyrivibrio proteoclasticus	strain=B316	GCA_000145035.1	43305	43305	type	True	100.0	1465	1466	95	conclusive
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	80.2188	406	1466	95	below_threshold
Butyrivibrio fibrisolvens	strain=DSM 3071	GCA_900129945.1	831	831	suspected-type	True	79.6675	218	1466	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	78.4486	62	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:46,458] [INFO] DFAST Taxonomy check result was written to GCF_000145035.1_ASM14503v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:46,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:46,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:46,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference/checkm_data
[2024-01-24 14:19:46,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:46,541] [INFO] Task started: CheckM
[2024-01-24 14:19:46,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000145035.1_ASM14503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000145035.1_ASM14503v1_genomic.fna/checkm_input GCF_000145035.1_ASM14503v1_genomic.fna/checkm_result
[2024-01-24 14:20:25,126] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:25,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:25,149] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:25,149] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:25,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000145035.1_ASM14503v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:25,150] [INFO] Task started: Blastn
[2024-01-24 14:20:25,150] [INFO] Running command: blastn -query GCF_000145035.1_ASM14503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3d60d24-10ee-4f2c-8996-6b1f9b353fe6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000145035.1_ASM14503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:27,732] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:27,739] [INFO] Selected 15 target genomes.
[2024-01-24 14:20:27,739] [INFO] Target genome list was writen to GCF_000145035.1_ASM14503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:27,754] [INFO] Task started: fastANI
[2024-01-24 14:20:27,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdc1987e-9847-4802-a142-228dc7f8aba5/GCF_000145035.1_ASM14503v1_genomic.fna.gz --refList GCF_000145035.1_ASM14503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000145035.1_ASM14503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:39,350] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:39,378] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:39,379] [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_000145035.1	s__Butyrivibrio proteoclasticus	100.0	1466	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	97.35	97.35	0.84	0.84	2	conclusive
GCA_017433805.1	s__Butyrivibrio sp017433805	84.1745	781	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420945.1	s__Butyrivibrio sp000420945	83.4871	762	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102515.1	s__Butyrivibrio sp900102515	81.7218	674	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.65	95.65	0.82	0.82	2	-
GCF_900112195.1	s__Butyrivibrio sp900112195	81.0876	537	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622085.1	s__Butyrivibrio proteoclasticus_A	80.8956	413	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108105.1	s__Butyrivibrio sp900108105	80.5923	435	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103635.1	s__Butyrivibrio sp900103635	80.3946	404	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.99	95.99	0.85	0.85	2	-
GCA_015056685.1	s__Butyrivibrio sp015056685	80.016	426	1466	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	95.83	95.83	0.67	0.67	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,381] [INFO] GTDB search result was written to GCF_000145035.1_ASM14503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:39,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:39,385] [INFO] DFAST_QC result json was written to GCF_000145035.1_ASM14503v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:39,385] [INFO] DFAST_QC completed!
[2024-01-24 14:20:39,385] [INFO] Total running time: 0h1m24s