[2023-06-08 08:10:35,440] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:10:35,442] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:10:35,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference
[2023-06-08 08:10:36,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:10:36,685] [INFO] Task started: Prodigal
[2023-06-08 08:10:36,685] [INFO] Running command: gunzip -c /var/lib/cwl/stgaca0d36f-1753-4014-9b32-8ebaf0449306/GCA_945897105.1_TE-08apr19-162_genomic.fna.gz | prodigal -d GCA_945897105.1_TE-08apr19-162_genomic.fna/cds.fna -a GCA_945897105.1_TE-08apr19-162_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:10:42,269] [INFO] Task succeeded: Prodigal
[2023-06-08 08:10:42,269] [INFO] Task started: HMMsearch
[2023-06-08 08:10:42,270] [INFO] Running command: hmmsearch --tblout GCA_945897105.1_TE-08apr19-162_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference/reference_markers.hmm GCA_945897105.1_TE-08apr19-162_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:10:42,545] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:10:42,546] [INFO] Found 6/6 markers.
[2023-06-08 08:10:42,568] [INFO] Query marker FASTA was written to GCA_945897105.1_TE-08apr19-162_genomic.fna/markers.fasta
[2023-06-08 08:10:42,569] [INFO] Task started: Blastn
[2023-06-08 08:10:42,569] [INFO] Running command: blastn -query GCA_945897105.1_TE-08apr19-162_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference/reference_markers.fasta -out GCA_945897105.1_TE-08apr19-162_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:10:43,173] [INFO] Task succeeded: Blastn
[2023-06-08 08:10:43,177] [INFO] Selected 21 target genomes.
[2023-06-08 08:10:43,178] [INFO] Target genome list was writen to GCA_945897105.1_TE-08apr19-162_genomic.fna/target_genomes.txt
[2023-06-08 08:10:43,180] [INFO] Task started: fastANI
[2023-06-08 08:10:43,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca0d36f-1753-4014-9b32-8ebaf0449306/GCA_945897105.1_TE-08apr19-162_genomic.fna.gz --refList GCA_945897105.1_TE-08apr19-162_genomic.fna/target_genomes.txt --output GCA_945897105.1_TE-08apr19-162_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:10:54,684] [INFO] Task succeeded: fastANI
[2023-06-08 08:10:54,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:10:54,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:10:54,688] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:10:54,688] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:10:54,688] [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
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	75.2367	50	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:10:54,690] [INFO] DFAST Taxonomy check result was written to GCA_945897105.1_TE-08apr19-162_genomic.fna/tc_result.tsv
[2023-06-08 08:10:54,691] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:10:54,691] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:10:54,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference/checkm_data
[2023-06-08 08:10:54,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:10:54,721] [INFO] Task started: CheckM
[2023-06-08 08:10:54,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897105.1_TE-08apr19-162_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897105.1_TE-08apr19-162_genomic.fna/checkm_input GCA_945897105.1_TE-08apr19-162_genomic.fna/checkm_result
[2023-06-08 08:11:18,607] [INFO] Task succeeded: CheckM
[2023-06-08 08:11:18,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 11.57%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2023-06-08 08:11:18,634] [INFO] ===== Completeness check finished =====
[2023-06-08 08:11:18,635] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:11:18,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897105.1_TE-08apr19-162_genomic.fna/markers.fasta)
[2023-06-08 08:11:18,636] [INFO] Task started: Blastn
[2023-06-08 08:11:18,636] [INFO] Running command: blastn -query GCA_945897105.1_TE-08apr19-162_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbfa9412-b815-429d-b7a4-6e5beac28649/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897105.1_TE-08apr19-162_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:11:19,459] [INFO] Task succeeded: Blastn
[2023-06-08 08:11:19,464] [INFO] Selected 16 target genomes.
[2023-06-08 08:11:19,464] [INFO] Target genome list was writen to GCA_945897105.1_TE-08apr19-162_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:11:19,466] [INFO] Task started: fastANI
[2023-06-08 08:11:19,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca0d36f-1753-4014-9b32-8ebaf0449306/GCA_945897105.1_TE-08apr19-162_genomic.fna.gz --refList GCA_945897105.1_TE-08apr19-162_genomic.fna/target_genomes_gtdb.txt --output GCA_945897105.1_TE-08apr19-162_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:11:28,554] [INFO] Task succeeded: fastANI
[2023-06-08 08:11:28,577] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 08:11:28,578] [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_005787585.1	s__UBA2475 sp005787585	89.5879	398	620	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	77.5081	96	620	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_013288385.1	s__UBA2475 sp013288385	77.307	54	620	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_903928655.1	s__UBA4416 sp903928655	77.1854	105	620	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_002342065.1	s__UBA2475 sp002342065	76.9025	127	620	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	76.7918	145	620	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	76.744	133	620	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_016787785.1	s__UBA2475 sp016787785	76.6597	129	620	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_016715905.1	s__UBA2475 sp016715905	76.615	80	620	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	76.5169	88	620	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_903893815.1	s__UBA4416 sp903893815	76.4738	96	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	97.38	96.70	0.85	0.80	6	-
GCA_016711805.1	s__UBA4416 sp016711805	76.3762	105	620	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_013298715.1	s__UBA2475 sp013298715	76.2285	117	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA2475	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:11:28,580] [INFO] GTDB search result was written to GCA_945897105.1_TE-08apr19-162_genomic.fna/result_gtdb.tsv
[2023-06-08 08:11:28,581] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:11:28,584] [INFO] DFAST_QC result json was written to GCA_945897105.1_TE-08apr19-162_genomic.fna/dqc_result.json
[2023-06-08 08:11:28,584] [INFO] DFAST_QC completed!
[2023-06-08 08:11:28,584] [INFO] Total running time: 0h0m53s