[2024-01-24 13:18:28,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:28,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:28,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference
[2024-01-24 13:18:30,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:30,038] [INFO] Task started: Prodigal
[2024-01-24 13:18:30,038] [INFO] Running command: gunzip -c /var/lib/cwl/stgd183f61a-5faf-4417-bc07-3994a333715d/GCF_014287455.1_ASM1428745v1_genomic.fna.gz | prodigal -d GCF_014287455.1_ASM1428745v1_genomic.fna/cds.fna -a GCF_014287455.1_ASM1428745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:02,054] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:02,055] [INFO] Task started: HMMsearch
[2024-01-24 13:19:02,055] [INFO] Running command: hmmsearch --tblout GCF_014287455.1_ASM1428745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference/reference_markers.hmm GCF_014287455.1_ASM1428745v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:02,417] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:02,418] [INFO] Found 6/6 markers.
[2024-01-24 13:19:02,470] [INFO] Query marker FASTA was written to GCF_014287455.1_ASM1428745v1_genomic.fna/markers.fasta
[2024-01-24 13:19:02,471] [INFO] Task started: Blastn
[2024-01-24 13:19:02,471] [INFO] Running command: blastn -query GCF_014287455.1_ASM1428745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference/reference_markers.fasta -out GCF_014287455.1_ASM1428745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,177] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:03,177] [INFO] Target genome list was writen to GCF_014287455.1_ASM1428745v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:03,195] [INFO] Task started: fastANI
[2024-01-24 13:19:03,195] [INFO] Running command: fastANI --query /var/lib/cwl/stgd183f61a-5faf-4417-bc07-3994a333715d/GCF_014287455.1_ASM1428745v1_genomic.fna.gz --refList GCF_014287455.1_ASM1428745v1_genomic.fna/target_genomes.txt --output GCF_014287455.1_ASM1428745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:16,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:16,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:16,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:16,658] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:16,659] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:16,659] [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
Butyricimonas synergistica	strain=DSM 23225	GCA_000379665.1	544644	544644	type	True	83.4234	1008	1777	95	below_threshold
Butyricimonas faecalis	strain=vagina	GCA_900258545.1	2093856	2093856	type	True	80.4217	598	1777	95	below_threshold
Butyricimonas faecalis	strain=H184	GCA_003991565.1	2093856	2093856	type	True	80.2891	586	1777	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	79.9445	653	1777	95	below_threshold
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	79.9325	652	1777	95	below_threshold
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	79.9125	652	1777	95	below_threshold
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	79.8307	671	1777	95	below_threshold
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	79.8307	664	1777	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	79.7054	606	1777	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_000519105.1	544645	544645	type	True	79.5714	606	1777	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	78.9232	59	1777	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	78.8453	61	1777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:16,661] [INFO] DFAST Taxonomy check result was written to GCF_014287455.1_ASM1428745v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:16,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:16,661] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:16,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference/checkm_data
[2024-01-24 13:19:16,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:16,715] [INFO] Task started: CheckM
[2024-01-24 13:19:16,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287455.1_ASM1428745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287455.1_ASM1428745v1_genomic.fna/checkm_input GCF_014287455.1_ASM1428745v1_genomic.fna/checkm_result
[2024-01-24 13:20:36,901] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:36,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:36,926] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:36,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:36,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287455.1_ASM1428745v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:36,928] [INFO] Task started: Blastn
[2024-01-24 13:20:36,928] [INFO] Running command: blastn -query GCF_014287455.1_ASM1428745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e852013-4f25-4c47-b5bf-7cd4c969826d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287455.1_ASM1428745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:37,774] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:37,778] [INFO] Selected 11 target genomes.
[2024-01-24 13:20:37,779] [INFO] Target genome list was writen to GCF_014287455.1_ASM1428745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:37,837] [INFO] Task started: fastANI
[2024-01-24 13:20:37,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgd183f61a-5faf-4417-bc07-3994a333715d/GCF_014287455.1_ASM1428745v1_genomic.fna.gz --refList GCF_014287455.1_ASM1428745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287455.1_ASM1428745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:48,334] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:48,349] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:48,350] [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_900184685.1	s__Butyricimonas sp900184685	97.6878	1414	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	97.37	96.90	0.86	0.81	4	conclusive
GCA_900759925.1	s__Butyricimonas sp900759925	83.6856	930	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379665.1	s__Butyricimonas synergistica	83.4235	1009	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.02	98.02	0.85	0.85	3	-
GCF_003991565.1	s__Butyricimonas faecalis	80.3106	583	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	-
GCF_014647335.1	s__Butyricimonas faecihominis	79.952	648	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCF_011927845.1	s__Butyricimonas paravirosa	79.8	670	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	-
GCF_003479425.1	s__Butyricimonas sp003479425	79.6354	665	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
GCF_000519105.1	s__Butyricimonas virosa	79.5699	607	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCA_900761485.1	s__Butyricimonas sp900761485	78.8394	448	1777	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:48,351] [INFO] GTDB search result was written to GCF_014287455.1_ASM1428745v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:48,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:48,357] [INFO] DFAST_QC result json was written to GCF_014287455.1_ASM1428745v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:48,358] [INFO] DFAST_QC completed!
[2024-01-24 13:20:48,358] [INFO] Total running time: 0h2m20s