[2023-06-17 00:12:20,060] [INFO] DFAST_QC pipeline started.
[2023-06-17 00:12:20,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 00:12:20,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference
[2023-06-17 00:12:21,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 00:12:21,326] [INFO] Task started: Prodigal
[2023-06-17 00:12:21,326] [INFO] Running command: gunzip -c /var/lib/cwl/stged337f43-e66c-408c-8a07-a665e821550e/GCA_009885445.1_ASM988544v1_genomic.fna.gz | prodigal -d GCA_009885445.1_ASM988544v1_genomic.fna/cds.fna -a GCA_009885445.1_ASM988544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 00:12:28,904] [INFO] Task succeeded: Prodigal
[2023-06-17 00:12:28,905] [INFO] Task started: HMMsearch
[2023-06-17 00:12:28,905] [INFO] Running command: hmmsearch --tblout GCA_009885445.1_ASM988544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference/reference_markers.hmm GCA_009885445.1_ASM988544v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 00:12:29,148] [INFO] Task succeeded: HMMsearch
[2023-06-17 00:12:29,152] [INFO] Found 6/6 markers.
[2023-06-17 00:12:29,187] [INFO] Query marker FASTA was written to GCA_009885445.1_ASM988544v1_genomic.fna/markers.fasta
[2023-06-17 00:12:29,187] [INFO] Task started: Blastn
[2023-06-17 00:12:29,187] [INFO] Running command: blastn -query GCA_009885445.1_ASM988544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference/reference_markers.fasta -out GCA_009885445.1_ASM988544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:12:29,860] [INFO] Task succeeded: Blastn
[2023-06-17 00:12:29,870] [INFO] Selected 29 target genomes.
[2023-06-17 00:12:29,871] [INFO] Target genome list was writen to GCA_009885445.1_ASM988544v1_genomic.fna/target_genomes.txt
[2023-06-17 00:12:29,886] [INFO] Task started: fastANI
[2023-06-17 00:12:29,886] [INFO] Running command: fastANI --query /var/lib/cwl/stged337f43-e66c-408c-8a07-a665e821550e/GCA_009885445.1_ASM988544v1_genomic.fna.gz --refList GCA_009885445.1_ASM988544v1_genomic.fna/target_genomes.txt --output GCA_009885445.1_ASM988544v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 00:12:44,370] [INFO] Task succeeded: fastANI
[2023-06-17 00:12:44,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 00:12:44,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 00:12:44,374] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 00:12:44,374] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 00:12:44,375] [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
--------------------------------------------------------------------------------
[2023-06-17 00:12:44,381] [INFO] DFAST Taxonomy check result was written to GCA_009885445.1_ASM988544v1_genomic.fna/tc_result.tsv
[2023-06-17 00:12:44,381] [INFO] ===== Taxonomy check completed =====
[2023-06-17 00:12:44,382] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 00:12:44,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference/checkm_data
[2023-06-17 00:12:44,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 00:12:44,429] [INFO] Task started: CheckM
[2023-06-17 00:12:44,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009885445.1_ASM988544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009885445.1_ASM988544v1_genomic.fna/checkm_input GCA_009885445.1_ASM988544v1_genomic.fna/checkm_result
[2023-06-17 00:13:12,588] [INFO] Task succeeded: CheckM
[2023-06-17 00:13:12,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 00:13:12,613] [INFO] ===== Completeness check finished =====
[2023-06-17 00:13:12,614] [INFO] ===== Start GTDB Search =====
[2023-06-17 00:13:12,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009885445.1_ASM988544v1_genomic.fna/markers.fasta)
[2023-06-17 00:13:12,615] [INFO] Task started: Blastn
[2023-06-17 00:13:12,615] [INFO] Running command: blastn -query GCA_009885445.1_ASM988544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93ec384c-99af-423e-9c3e-676ec1c57a5d/dqc_reference/reference_markers_gtdb.fasta -out GCA_009885445.1_ASM988544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:13:13,735] [INFO] Task succeeded: Blastn
[2023-06-17 00:13:13,741] [INFO] Selected 21 target genomes.
[2023-06-17 00:13:13,741] [INFO] Target genome list was writen to GCA_009885445.1_ASM988544v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 00:13:13,751] [INFO] Task started: fastANI
[2023-06-17 00:13:13,751] [INFO] Running command: fastANI --query /var/lib/cwl/stged337f43-e66c-408c-8a07-a665e821550e/GCA_009885445.1_ASM988544v1_genomic.fna.gz --refList GCA_009885445.1_ASM988544v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009885445.1_ASM988544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 00:13:26,863] [INFO] Task succeeded: fastANI
[2023-06-17 00:13:26,880] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 00:13:26,881] [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_009885445.1	s__UBA7227 sp009885445	100.0	771	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016234485.1	s__UBA7227 sp016234485	77.1606	236	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002473085.1	s__UBA7227 sp002473085	77.0886	156	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	98.42	98.07	0.85	0.72	10	-
GCA_019187665.1	s__UBA7227 sp019187665	77.0815	191	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003598975.1	s__UBA7227 sp003598975	76.9752	163	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716235.1	s__UBA12294 sp016716235	76.536	142	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	98.53	97.10	0.95	0.94	3	-
GCA_016213105.1	s__JACPVF01 sp016213105	76.5095	134	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JACPVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191985.1	s__OLB14 sp016191985	76.2974	68	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714565.1	s__OLB14 sp016714565	76.219	79	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703605.1	s__OLB14 sp016703605	76.219	111	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.59	98.59	0.83	0.83	2	-
GCA_016932715.1	s__UBA12294 sp016932715	76.179	58	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715195.1	s__OLB14 sp016715195	76.1224	86	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	97.24	96.60	0.91	0.90	3	-
GCA_016235445.1	s__OLB14 sp016235445	76.0781	137	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219545.1	s__OLB14 sp016219545	76.0092	67	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343775.1	s__OLB14 sp002343775	75.8794	73	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	99.89	99.61	0.98	0.94	7	-
GCA_017985935.1	s__OLB14 sp017985935	75.6928	64	783	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	99.53	99.53	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-17 00:13:26,883] [INFO] GTDB search result was written to GCA_009885445.1_ASM988544v1_genomic.fna/result_gtdb.tsv
[2023-06-17 00:13:26,884] [INFO] ===== GTDB Search completed =====
[2023-06-17 00:13:26,887] [INFO] DFAST_QC result json was written to GCA_009885445.1_ASM988544v1_genomic.fna/dqc_result.json
[2023-06-17 00:13:26,887] [INFO] DFAST_QC completed!
[2023-06-17 00:13:26,887] [INFO] Total running time: 0h1m7s