[2023-06-17 06:59:58,584] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:59:58,589] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:59:58,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference
[2023-06-17 07:00:00,076] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:00:00,080] [INFO] Task started: Prodigal
[2023-06-17 07:00:00,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e1eb6e0-8d1e-4875-94e1-d77a02f3d65e/GCA_028708775.1_ASM2870877v1_genomic.fna.gz | prodigal -d GCA_028708775.1_ASM2870877v1_genomic.fna/cds.fna -a GCA_028708775.1_ASM2870877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:00:04,597] [INFO] Task succeeded: Prodigal
[2023-06-17 07:00:04,598] [INFO] Task started: HMMsearch
[2023-06-17 07:00:04,598] [INFO] Running command: hmmsearch --tblout GCA_028708775.1_ASM2870877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference/reference_markers.hmm GCA_028708775.1_ASM2870877v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:00:04,849] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:00:04,850] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7e1eb6e0-8d1e-4875-94e1-d77a02f3d65e/GCA_028708775.1_ASM2870877v1_genomic.fna.gz]
[2023-06-17 07:00:04,874] [INFO] Query marker FASTA was written to GCA_028708775.1_ASM2870877v1_genomic.fna/markers.fasta
[2023-06-17 07:00:04,874] [INFO] Task started: Blastn
[2023-06-17 07:00:04,874] [INFO] Running command: blastn -query GCA_028708775.1_ASM2870877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference/reference_markers.fasta -out GCA_028708775.1_ASM2870877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:00:05,437] [INFO] Task succeeded: Blastn
[2023-06-17 07:00:05,441] [INFO] Selected 10 target genomes.
[2023-06-17 07:00:05,442] [INFO] Target genome list was writen to GCA_028708775.1_ASM2870877v1_genomic.fna/target_genomes.txt
[2023-06-17 07:00:05,444] [INFO] Task started: fastANI
[2023-06-17 07:00:05,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1eb6e0-8d1e-4875-94e1-d77a02f3d65e/GCA_028708775.1_ASM2870877v1_genomic.fna.gz --refList GCA_028708775.1_ASM2870877v1_genomic.fna/target_genomes.txt --output GCA_028708775.1_ASM2870877v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:00:13,029] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:13,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:00:13,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:00:13,036] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-17 07:00:13,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 07:00:13,036] [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
Syntrophaceticus schinkii	strain=Sp3	GCA_000946815.1	499207	499207	type	True	98.98	539	581	95	conclusive
Thermacetogenium phaeum	strain=DSM 12270	GCA_000519285.1	85874	85874	type	True	76.5126	60	581	95	below_threshold
Thermacetogenium phaeum	strain=DSM 12270	GCA_000305935.1	85874	85874	type	True	76.4413	57	581	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:00:13,063] [INFO] DFAST Taxonomy check result was written to GCA_028708775.1_ASM2870877v1_genomic.fna/tc_result.tsv
[2023-06-17 07:00:13,064] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:00:13,064] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:00:13,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference/checkm_data
[2023-06-17 07:00:13,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:00:13,089] [INFO] Task started: CheckM
[2023-06-17 07:00:13,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708775.1_ASM2870877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708775.1_ASM2870877v1_genomic.fna/checkm_input GCA_028708775.1_ASM2870877v1_genomic.fna/checkm_result
[2023-06-17 07:00:33,598] [INFO] Task succeeded: CheckM
[2023-06-17 07:00:33,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.45%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 07:00:33,626] [INFO] ===== Completeness check finished =====
[2023-06-17 07:00:33,626] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:00:33,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708775.1_ASM2870877v1_genomic.fna/markers.fasta)
[2023-06-17 07:00:33,627] [INFO] Task started: Blastn
[2023-06-17 07:00:33,627] [INFO] Running command: blastn -query GCA_028708775.1_ASM2870877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91cee190-ab54-4051-9f84-9c84beb0aaa7/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708775.1_ASM2870877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:00:34,398] [INFO] Task succeeded: Blastn
[2023-06-17 07:00:34,403] [INFO] Selected 8 target genomes.
[2023-06-17 07:00:34,403] [INFO] Target genome list was writen to GCA_028708775.1_ASM2870877v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:00:34,409] [INFO] Task started: fastANI
[2023-06-17 07:00:34,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1eb6e0-8d1e-4875-94e1-d77a02f3d65e/GCA_028708775.1_ASM2870877v1_genomic.fna.gz --refList GCA_028708775.1_ASM2870877v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708775.1_ASM2870877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:00:38,115] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:38,123] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:00:38,123] [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_000946815.1	s__Syntrophaceticus schinkii	98.98	539	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Syntrophaceticus	95.0	98.42	98.16	0.86	0.84	3	conclusive
GCA_012839645.1	s__Syntrophaceticus sp012839645	85.0026	349	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Syntrophaceticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002397275.1	s__Syntrophaceticus sp002397275	78.6678	223	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Syntrophaceticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426495.1	s__Syntrophaceticus sp002426495	78.556	223	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Syntrophaceticus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012840405.1	s__DTU068 sp012840405	77.8455	120	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__DTU068	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001513545.1	s__DTU068 sp001513545	77.6925	135	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__DTU068	95.0	99.53	99.44	0.89	0.88	3	-
GCF_000305935.1	s__Thermacetogenium phaeum	76.4413	57	581	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Thermacetogeniales;f__Thermacetogeniaceae;g__Thermacetogenium	95.0	98.55	97.17	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2023-06-17 07:00:38,125] [INFO] GTDB search result was written to GCA_028708775.1_ASM2870877v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:00:38,126] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:00:38,129] [INFO] DFAST_QC result json was written to GCA_028708775.1_ASM2870877v1_genomic.fna/dqc_result.json
[2023-06-17 07:00:38,129] [INFO] DFAST_QC completed!
[2023-06-17 07:00:38,129] [INFO] Total running time: 0h0m40s