[2023-06-19 02:25:11,346] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:25:11,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:25:11,360] [INFO] DQC Reference Directory: /var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference
[2023-06-19 02:25:12,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:25:12,583] [INFO] Task started: Prodigal
[2023-06-19 02:25:12,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg168dac62-61fa-4c8b-9cc0-2697fc5c7e9e/GCA_018267655.1_ASM1826765v1_genomic.fna.gz | prodigal -d GCA_018267655.1_ASM1826765v1_genomic.fna/cds.fna -a GCA_018267655.1_ASM1826765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:23,202] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:23,203] [INFO] Task started: HMMsearch
[2023-06-19 02:25:23,203] [INFO] Running command: hmmsearch --tblout GCA_018267655.1_ASM1826765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference/reference_markers.hmm GCA_018267655.1_ASM1826765v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:23,479] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:23,481] [INFO] Found 6/6 markers.
[2023-06-19 02:25:23,544] [INFO] Query marker FASTA was written to GCA_018267655.1_ASM1826765v1_genomic.fna/markers.fasta
[2023-06-19 02:25:23,545] [INFO] Task started: Blastn
[2023-06-19 02:25:23,545] [INFO] Running command: blastn -query GCA_018267655.1_ASM1826765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference/reference_markers.fasta -out GCA_018267655.1_ASM1826765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:24,120] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:24,125] [INFO] Selected 28 target genomes.
[2023-06-19 02:25:24,126] [INFO] Target genome list was writen to GCA_018267655.1_ASM1826765v1_genomic.fna/target_genomes.txt
[2023-06-19 02:25:24,128] [INFO] Task started: fastANI
[2023-06-19 02:25:24,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg168dac62-61fa-4c8b-9cc0-2697fc5c7e9e/GCA_018267655.1_ASM1826765v1_genomic.fna.gz --refList GCA_018267655.1_ASM1826765v1_genomic.fna/target_genomes.txt --output GCA_018267655.1_ASM1826765v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:40,487] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:40,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:40,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:40,490] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:40,491] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 02:25:40,491] [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
--------------------------------------------------------------------------------
[2023-06-19 02:25:40,494] [INFO] DFAST Taxonomy check result was written to GCA_018267655.1_ASM1826765v1_genomic.fna/tc_result.tsv
[2023-06-19 02:25:40,494] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:40,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:40,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference/checkm_data
[2023-06-19 02:25:40,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:40,538] [INFO] Task started: CheckM
[2023-06-19 02:25:40,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018267655.1_ASM1826765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018267655.1_ASM1826765v1_genomic.fna/checkm_input GCA_018267655.1_ASM1826765v1_genomic.fna/checkm_result
[2023-06-19 02:26:15,885] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:15,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:15,908] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:15,908] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:15,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018267655.1_ASM1826765v1_genomic.fna/markers.fasta)
[2023-06-19 02:26:15,909] [INFO] Task started: Blastn
[2023-06-19 02:26:15,909] [INFO] Running command: blastn -query GCA_018267655.1_ASM1826765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac1ab620-b799-4186-9e59-52927feec9f9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018267655.1_ASM1826765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:16,679] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:16,685] [INFO] Selected 21 target genomes.
[2023-06-19 02:26:16,685] [INFO] Target genome list was writen to GCA_018267655.1_ASM1826765v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:16,688] [INFO] Task started: fastANI
[2023-06-19 02:26:16,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg168dac62-61fa-4c8b-9cc0-2697fc5c7e9e/GCA_018267655.1_ASM1826765v1_genomic.fna.gz --refList GCA_018267655.1_ASM1826765v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018267655.1_ASM1826765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:29,542] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:29,558] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:26:29,559] [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_018267655.1	s__UBA2475 sp018267655	100.0	1078	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016715905.1	s__UBA2475 sp016715905	76.4676	112	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787705.1	s__UBA2475 sp016787705	76.4368	118	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342065.1	s__UBA2475 sp002342065	76.323	109	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298715.1	s__UBA2475 sp013298715	76.2495	167	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319075.1	s__UBA2475 sp002319075	76.1659	65	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709575.1	s__JAFLBH01 sp016709575	76.1538	101	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288385.1	s__UBA2475 sp013288385	76.1102	65	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420145.1	s__UBA4416 sp002420145	76.0913	90	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787445.1	s__JAFLBH01 sp016787445	76.0678	83	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__JAFLBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297775.1	s__UBA2475 sp013297775	76.0327	94	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705695.1	s__UBA2475 sp016705695	75.8466	88	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	96.82	95.10	0.91	0.90	4	-
GCA_903923915.1	s__PALSA-968 sp903923915	75.7825	64	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__PALSA-968	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787785.1	s__UBA2475 sp016787785	75.7104	88	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697245.1	s__UBA2475 sp013697245	75.6928	111	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185125.1	s__UBA2475 sp016185125	75.688	105	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816615.1	s__UBA2475 sp013816615	75.5493	119	1085	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:29,561] [INFO] GTDB search result was written to GCA_018267655.1_ASM1826765v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:29,561] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:29,565] [INFO] DFAST_QC result json was written to GCA_018267655.1_ASM1826765v1_genomic.fna/dqc_result.json
[2023-06-19 02:26:29,565] [INFO] DFAST_QC completed!
[2023-06-19 02:26:29,565] [INFO] Total running time: 0h1m18s