[2023-06-28 00:18:38,203] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:18:38,205] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:18:38,205] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference
[2023-06-28 00:18:39,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:18:39,423] [INFO] Task started: Prodigal
[2023-06-28 00:18:39,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e6a65fa-8d87-4d77-aae5-9ebff1b5c8ab/GCA_002449655.1_ASM244965v1_genomic.fna.gz | prodigal -d GCA_002449655.1_ASM244965v1_genomic.fna/cds.fna -a GCA_002449655.1_ASM244965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:18:48,427] [INFO] Task succeeded: Prodigal
[2023-06-28 00:18:48,427] [INFO] Task started: HMMsearch
[2023-06-28 00:18:48,427] [INFO] Running command: hmmsearch --tblout GCA_002449655.1_ASM244965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference/reference_markers.hmm GCA_002449655.1_ASM244965v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:18:48,667] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:18:48,669] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2e6a65fa-8d87-4d77-aae5-9ebff1b5c8ab/GCA_002449655.1_ASM244965v1_genomic.fna.gz]
[2023-06-28 00:18:48,699] [INFO] Query marker FASTA was written to GCA_002449655.1_ASM244965v1_genomic.fna/markers.fasta
[2023-06-28 00:18:48,699] [INFO] Task started: Blastn
[2023-06-28 00:18:48,699] [INFO] Running command: blastn -query GCA_002449655.1_ASM244965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference/reference_markers.fasta -out GCA_002449655.1_ASM244965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:18:49,212] [INFO] Task succeeded: Blastn
[2023-06-28 00:18:49,243] [INFO] Selected 10 target genomes.
[2023-06-28 00:18:49,243] [INFO] Target genome list was writen to GCA_002449655.1_ASM244965v1_genomic.fna/target_genomes.txt
[2023-06-28 00:18:49,247] [INFO] Task started: fastANI
[2023-06-28 00:18:49,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e6a65fa-8d87-4d77-aae5-9ebff1b5c8ab/GCA_002449655.1_ASM244965v1_genomic.fna.gz --refList GCA_002449655.1_ASM244965v1_genomic.fna/target_genomes.txt --output GCA_002449655.1_ASM244965v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:18:54,728] [INFO] Task succeeded: fastANI
[2023-06-28 00:18:54,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:18:54,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:18:54,735] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2023-06-28 00:18:54,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 00:18:54,736] [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
Prevotella bryantii	strain=DSM 11371	GCA_019973295.1	77095	77095	type	True	99.1742	573	616	95	conclusive
Prevotella bryantii	strain=B14	GCA_900110745.1	77095	77095	type	True	99.1231	573	616	95	conclusive
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	99.118	575	616	95	conclusive
Prevotella bryantii	strain=B14	GCA_000179055.1	77095	77095	type	True	99.0941	558	616	95	conclusive
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.9309	91	616	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.9235	72	616	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:18:54,738] [INFO] DFAST Taxonomy check result was written to GCA_002449655.1_ASM244965v1_genomic.fna/tc_result.tsv
[2023-06-28 00:18:54,739] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:18:54,739] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:18:54,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference/checkm_data
[2023-06-28 00:18:54,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:18:54,769] [INFO] Task started: CheckM
[2023-06-28 00:18:54,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002449655.1_ASM244965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002449655.1_ASM244965v1_genomic.fna/checkm_input GCA_002449655.1_ASM244965v1_genomic.fna/checkm_result
[2023-06-28 00:19:26,867] [INFO] Task succeeded: CheckM
[2023-06-28 00:19:26,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:19:26,891] [INFO] ===== Completeness check finished =====
[2023-06-28 00:19:26,891] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:19:26,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002449655.1_ASM244965v1_genomic.fna/markers.fasta)
[2023-06-28 00:19:26,892] [INFO] Task started: Blastn
[2023-06-28 00:19:26,892] [INFO] Running command: blastn -query GCA_002449655.1_ASM244965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5243973-92cf-49b2-9fd7-79d4634c7b15/dqc_reference/reference_markers_gtdb.fasta -out GCA_002449655.1_ASM244965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:19:27,411] [INFO] Task succeeded: Blastn
[2023-06-28 00:19:27,428] [INFO] Selected 15 target genomes.
[2023-06-28 00:19:27,428] [INFO] Target genome list was writen to GCA_002449655.1_ASM244965v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:19:27,439] [INFO] Task started: fastANI
[2023-06-28 00:19:27,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e6a65fa-8d87-4d77-aae5-9ebff1b5c8ab/GCA_002449655.1_ASM244965v1_genomic.fna.gz --refList GCA_002449655.1_ASM244965v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002449655.1_ASM244965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:19:34,866] [INFO] Task succeeded: fastANI
[2023-06-28 00:19:34,881] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:19:34,882] [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_000179055.1	s__Prevotella bryantii	99.0941	558	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.02	98.58	0.88	0.73	13	conclusive
GCA_905236755.1	s__Prevotella sp905236755	77.4884	77	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.83	97.34	0.84	0.68	4	-
GCF_009495355.1	s__Prevotella sp900313215	77.438	51	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	-
GCA_902775075.1	s__Prevotella sp902775075	77.0006	80	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019127135.1	s__Prevotella sp900551275	76.9878	75	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_000426565.1	s__Prevotella albensis	76.9536	91	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000157935.1	s__Prevotella copri	76.8539	72	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_003483565.1	s__Prevotella sp003483565	76.806	87	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.31	99.31	0.72	0.72	2	-
GCA_018054505.1	s__Prevotella sp018054505	76.4935	75	616	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.05	98.05	0.52	0.52	2	-
--------------------------------------------------------------------------------
[2023-06-28 00:19:34,884] [INFO] GTDB search result was written to GCA_002449655.1_ASM244965v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:19:34,885] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:19:34,888] [INFO] DFAST_QC result json was written to GCA_002449655.1_ASM244965v1_genomic.fna/dqc_result.json
[2023-06-28 00:19:34,889] [INFO] DFAST_QC completed!
[2023-06-28 00:19:34,889] [INFO] Total running time: 0h0m57s