[2023-03-16 15:45:05,960] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:45:05,960] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:45:05,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference
[2023-03-16 15:45:07,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:45:07,299] [INFO] Task started: Prodigal
[2023-03-16 15:45:07,299] [INFO] Running command: cat /var/lib/cwl/stga1f1222d-7ffd-4e4d-88d9-686dfad0ff6f/OceanDNA-b5098.fa | prodigal -d OceanDNA-b5098/cds.fna -a OceanDNA-b5098/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:45:13,549] [INFO] Task succeeded: Prodigal
[2023-03-16 15:45:13,550] [INFO] Task started: HMMsearch
[2023-03-16 15:45:13,550] [INFO] Running command: hmmsearch --tblout OceanDNA-b5098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference/reference_markers.hmm OceanDNA-b5098/protein.faa > /dev/null
[2023-03-16 15:45:13,694] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:45:13,695] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga1f1222d-7ffd-4e4d-88d9-686dfad0ff6f/OceanDNA-b5098.fa]
[2023-03-16 15:45:13,702] [INFO] Query marker FASTA was written to OceanDNA-b5098/markers.fasta
[2023-03-16 15:45:13,702] [INFO] Task started: Blastn
[2023-03-16 15:45:13,702] [INFO] Running command: blastn -query OceanDNA-b5098/markers.fasta -db /var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference/reference_markers.fasta -out OceanDNA-b5098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:45:14,202] [INFO] Task succeeded: Blastn
[2023-03-16 15:45:14,203] [INFO] Selected 22 target genomes.
[2023-03-16 15:45:14,203] [INFO] Target genome list was writen to OceanDNA-b5098/target_genomes.txt
[2023-03-16 15:45:14,214] [INFO] Task started: fastANI
[2023-03-16 15:45:14,214] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f1222d-7ffd-4e4d-88d9-686dfad0ff6f/OceanDNA-b5098.fa --refList OceanDNA-b5098/target_genomes.txt --output OceanDNA-b5098/fastani_result.tsv --threads 1
[2023-03-16 15:45:32,692] [INFO] Task succeeded: fastANI
[2023-03-16 15:45:32,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:45:32,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:45:32,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:45:32,693] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 15:45:32,693] [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
--------------------------------------------------------------------------------
[2023-03-16 15:45:32,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5098/tc_result.tsv
[2023-03-16 15:45:32,693] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:45:32,693] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:45:32,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference/checkm_data
[2023-03-16 15:45:32,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:45:32,699] [INFO] Task started: CheckM
[2023-03-16 15:45:32,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5098/checkm_input OceanDNA-b5098/checkm_result
[2023-03-16 15:45:58,262] [INFO] Task succeeded: CheckM
[2023-03-16 15:45:58,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:45:58,264] [INFO] ===== Completeness check finished =====
[2023-03-16 15:45:58,264] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:45:58,264] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5098/markers.fasta)
[2023-03-16 15:45:58,264] [INFO] Task started: Blastn
[2023-03-16 15:45:58,264] [INFO] Running command: blastn -query OceanDNA-b5098/markers.fasta -db /var/lib/cwl/stg47e90853-f9e8-4ad8-a519-b41c67a8cbf6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:45:58,882] [INFO] Task succeeded: Blastn
[2023-03-16 15:45:58,883] [INFO] Selected 10 target genomes.
[2023-03-16 15:45:58,883] [INFO] Target genome list was writen to OceanDNA-b5098/target_genomes_gtdb.txt
[2023-03-16 15:45:59,431] [INFO] Task started: fastANI
[2023-03-16 15:45:59,431] [INFO] Running command: fastANI --query /var/lib/cwl/stga1f1222d-7ffd-4e4d-88d9-686dfad0ff6f/OceanDNA-b5098.fa --refList OceanDNA-b5098/target_genomes_gtdb.txt --output OceanDNA-b5098/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:46:02,032] [INFO] Task succeeded: fastANI
[2023-03-16 15:46:02,039] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 15:46:02,039] [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_018664745.1	s__UWMA-0277 sp018664745	99.6928	268	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014384505.1	s__UWMA-0277 sp014384505	81.4924	217	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	81.331	212	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_905478185.1	s__UWMA-0277 sp905478185	80.8837	210	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_905479165.1	s__UWMA-0277 sp905479165	80.2847	184	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182255.1	s__UWMA-0277 sp905182255	80.2816	123	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181635.1	s__UWMA-0277 sp905181635	80.2111	145	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	80.191	196	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	80.0204	208	327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:46:02,039] [INFO] GTDB search result was written to OceanDNA-b5098/result_gtdb.tsv
[2023-03-16 15:46:02,039] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:46:02,040] [INFO] DFAST_QC result json was written to OceanDNA-b5098/dqc_result.json
[2023-03-16 15:46:02,040] [INFO] DFAST_QC completed!
[2023-03-16 15:46:02,040] [INFO] Total running time: 0h0m56s