[2023-06-27 06:16:02,110] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:16:02,115] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:16:02,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference
[2023-06-27 06:16:04,817] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:16:04,818] [INFO] Task started: Prodigal
[2023-06-27 06:16:04,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg7025c870-f74f-45c5-aa48-e2fd5b2666fe/GCA_002314945.1_ASM231494v1_genomic.fna.gz | prodigal -d GCA_002314945.1_ASM231494v1_genomic.fna/cds.fna -a GCA_002314945.1_ASM231494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:16:20,758] [INFO] Task succeeded: Prodigal
[2023-06-27 06:16:20,759] [INFO] Task started: HMMsearch
[2023-06-27 06:16:20,759] [INFO] Running command: hmmsearch --tblout GCA_002314945.1_ASM231494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference/reference_markers.hmm GCA_002314945.1_ASM231494v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:16:20,989] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:16:20,991] [INFO] Found 6/6 markers.
[2023-06-27 06:16:21,041] [INFO] Query marker FASTA was written to GCA_002314945.1_ASM231494v1_genomic.fna/markers.fasta
[2023-06-27 06:16:21,041] [INFO] Task started: Blastn
[2023-06-27 06:16:21,042] [INFO] Running command: blastn -query GCA_002314945.1_ASM231494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference/reference_markers.fasta -out GCA_002314945.1_ASM231494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:16:21,645] [INFO] Task succeeded: Blastn
[2023-06-27 06:16:21,650] [INFO] Selected 26 target genomes.
[2023-06-27 06:16:21,650] [INFO] Target genome list was writen to GCA_002314945.1_ASM231494v1_genomic.fna/target_genomes.txt
[2023-06-27 06:16:21,658] [INFO] Task started: fastANI
[2023-06-27 06:16:21,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg7025c870-f74f-45c5-aa48-e2fd5b2666fe/GCA_002314945.1_ASM231494v1_genomic.fna.gz --refList GCA_002314945.1_ASM231494v1_genomic.fna/target_genomes.txt --output GCA_002314945.1_ASM231494v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:16:36,271] [INFO] Task succeeded: fastANI
[2023-06-27 06:16:36,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:16:36,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:16:36,273] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:16:36,273] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 06:16:36,274] [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
--------------------------------------------------------------------------------
[2023-06-27 06:16:36,276] [INFO] DFAST Taxonomy check result was written to GCA_002314945.1_ASM231494v1_genomic.fna/tc_result.tsv
[2023-06-27 06:16:36,276] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:16:36,277] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:16:36,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference/checkm_data
[2023-06-27 06:16:36,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:16:36,312] [INFO] Task started: CheckM
[2023-06-27 06:16:36,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002314945.1_ASM231494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002314945.1_ASM231494v1_genomic.fna/checkm_input GCA_002314945.1_ASM231494v1_genomic.fna/checkm_result
[2023-06-27 06:17:24,486] [INFO] Task succeeded: CheckM
[2023-06-27 06:17:24,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:17:24,507] [INFO] ===== Completeness check finished =====
[2023-06-27 06:17:24,508] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:17:24,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002314945.1_ASM231494v1_genomic.fna/markers.fasta)
[2023-06-27 06:17:24,508] [INFO] Task started: Blastn
[2023-06-27 06:17:24,509] [INFO] Running command: blastn -query GCA_002314945.1_ASM231494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da81ea7-305e-4cb4-ae27-1fa0affc5a01/dqc_reference/reference_markers_gtdb.fasta -out GCA_002314945.1_ASM231494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:17:25,335] [INFO] Task succeeded: Blastn
[2023-06-27 06:17:25,340] [INFO] Selected 27 target genomes.
[2023-06-27 06:17:25,340] [INFO] Target genome list was writen to GCA_002314945.1_ASM231494v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:17:25,351] [INFO] Task started: fastANI
[2023-06-27 06:17:25,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg7025c870-f74f-45c5-aa48-e2fd5b2666fe/GCA_002314945.1_ASM231494v1_genomic.fna.gz --refList GCA_002314945.1_ASM231494v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002314945.1_ASM231494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:17:38,177] [INFO] Task succeeded: fastANI
[2023-06-27 06:17:38,193] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:17:38,193] [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_002314945.1	s__UBA4372 sp002314945	100.0	838	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900543815.1	s__UBA4372 sp900543815	77.4023	81	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.82	97.58	0.92	0.88	4	-
GCA_017559845.1	s__UBA4372 sp017559845	77.252	67	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791675.1	s__UBA4372 sp902791675	77.0109	50	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427185.1	s__UBA4372 sp017427185	76.9586	80	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.11	97.78	0.90	0.84	7	-
GCA_017445925.1	s__UBA4372 sp017445925	76.9516	57	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541025.1	s__UBA4372 sp017541025	76.8312	61	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.17	97.17	0.84	0.84	2	-
GCA_902788315.1	s__UBA4372 sp902788315	76.7299	67	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.21	97.94	0.89	0.88	4	-
GCA_017525235.1	s__UBA4372 sp017525235	76.5667	58	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483665.1	s__UBA4372 sp017483665	76.2082	60	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292545.1	s__UBA4372 sp016292545	76.0802	59	846	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:17:38,195] [INFO] GTDB search result was written to GCA_002314945.1_ASM231494v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:17:38,196] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:17:38,281] [INFO] DFAST_QC result json was written to GCA_002314945.1_ASM231494v1_genomic.fna/dqc_result.json
[2023-06-27 06:17:38,281] [INFO] DFAST_QC completed!
[2023-06-27 06:17:38,281] [INFO] Total running time: 0h1m36s