[2023-03-16 03:23:47,623] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:47,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:47,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference
[2023-03-16 03:23:49,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:49,415] [INFO] Task started: Prodigal
[2023-03-16 03:23:49,415] [INFO] Running command: cat /var/lib/cwl/stg3495a4f9-9654-4e5b-ab58-49b0d96f29c9/OceanDNA-b46852.fa | prodigal -d OceanDNA-b46852/cds.fna -a OceanDNA-b46852/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:16,872] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:16,872] [INFO] Task started: HMMsearch
[2023-03-16 03:24:16,872] [INFO] Running command: hmmsearch --tblout OceanDNA-b46852/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference/reference_markers.hmm OceanDNA-b46852/protein.faa > /dev/null
[2023-03-16 03:24:17,093] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:17,094] [INFO] Found 6/6 markers.
[2023-03-16 03:24:17,116] [INFO] Query marker FASTA was written to OceanDNA-b46852/markers.fasta
[2023-03-16 03:24:17,117] [INFO] Task started: Blastn
[2023-03-16 03:24:17,117] [INFO] Running command: blastn -query OceanDNA-b46852/markers.fasta -db /var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference/reference_markers.fasta -out OceanDNA-b46852/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:17,629] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:17,630] [INFO] Selected 19 target genomes.
[2023-03-16 03:24:17,630] [INFO] Target genome list was writen to OceanDNA-b46852/target_genomes.txt
[2023-03-16 03:24:17,639] [INFO] Task started: fastANI
[2023-03-16 03:24:17,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg3495a4f9-9654-4e5b-ab58-49b0d96f29c9/OceanDNA-b46852.fa --refList OceanDNA-b46852/target_genomes.txt --output OceanDNA-b46852/fastani_result.tsv --threads 1
[2023-03-16 03:24:28,194] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:28,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:28,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:28,195] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:28,195] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:28,195] [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 03:24:28,212] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46852/tc_result.tsv
[2023-03-16 03:24:28,212] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:28,212] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:28,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference/checkm_data
[2023-03-16 03:24:28,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:28,223] [INFO] Task started: CheckM
[2023-03-16 03:24:28,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46852/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46852/checkm_input OceanDNA-b46852/checkm_result
[2023-03-16 03:25:37,514] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:37,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:37,516] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:37,517] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:37,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46852/markers.fasta)
[2023-03-16 03:25:37,518] [INFO] Task started: Blastn
[2023-03-16 03:25:37,518] [INFO] Running command: blastn -query OceanDNA-b46852/markers.fasta -db /var/lib/cwl/stg3f9d6cb7-5109-43c2-99df-e6be0c980c5c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46852/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:38,223] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:38,224] [INFO] Selected 14 target genomes.
[2023-03-16 03:25:38,224] [INFO] Target genome list was writen to OceanDNA-b46852/target_genomes_gtdb.txt
[2023-03-16 03:25:38,641] [INFO] Task started: fastANI
[2023-03-16 03:25:38,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg3495a4f9-9654-4e5b-ab58-49b0d96f29c9/OceanDNA-b46852.fa --refList OceanDNA-b46852/target_genomes_gtdb.txt --output OceanDNA-b46852/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:47,671] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:47,675] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:25:47,676] [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_002420315.1	s__SW10 sp002420315	99.4898	993	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.54	96.31	0.84	0.80	11	conclusive
GCA_905181965.1	s__SW10 sp905181965	87.9115	652	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.78	97.70	0.75	0.63	5	-
GCA_002323895.1	s__SW10 sp002323895	87.0197	925	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.17	98.66	0.86	0.81	3	-
GCA_000383735.1	s__SW10 sp000383735	86.188	501	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222765.1	s__SW10 sp018222765	78.3411	112	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002172625.1	s__SW10 sp002172625	77.8031	77	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:47,676] [INFO] GTDB search result was written to OceanDNA-b46852/result_gtdb.tsv
[2023-03-16 03:25:47,676] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:47,677] [INFO] DFAST_QC result json was written to OceanDNA-b46852/dqc_result.json
[2023-03-16 03:25:47,677] [INFO] DFAST_QC completed!
[2023-03-16 03:25:47,677] [INFO] Total running time: 0h2m0s