[2023-03-17 02:31:12,848] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference
[2023-03-17 02:31:14,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stg48f3eaa2-83ba-44a9-95c8-a376ce275791/OceanDNA-b6300.fa | prodigal -d OceanDNA-b6300/cds.fna -a OceanDNA-b6300/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:25,324] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:25,325] [INFO] Task started: HMMsearch
[2023-03-17 02:31:25,325] [INFO] Running command: hmmsearch --tblout OceanDNA-b6300/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference/reference_markers.hmm OceanDNA-b6300/protein.faa > /dev/null
[2023-03-17 02:31:25,499] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:25,500] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg48f3eaa2-83ba-44a9-95c8-a376ce275791/OceanDNA-b6300.fa]
[2023-03-17 02:31:25,515] [INFO] Query marker FASTA was written to OceanDNA-b6300/markers.fasta
[2023-03-17 02:31:25,516] [INFO] Task started: Blastn
[2023-03-17 02:31:25,516] [INFO] Running command: blastn -query OceanDNA-b6300/markers.fasta -db /var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference/reference_markers.fasta -out OceanDNA-b6300/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:26,066] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:26,067] [INFO] Selected 25 target genomes.
[2023-03-17 02:31:26,067] [INFO] Target genome list was writen to OceanDNA-b6300/target_genomes.txt
[2023-03-17 02:31:26,080] [INFO] Task started: fastANI
[2023-03-17 02:31:26,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f3eaa2-83ba-44a9-95c8-a376ce275791/OceanDNA-b6300.fa --refList OceanDNA-b6300/target_genomes.txt --output OceanDNA-b6300/fastani_result.tsv --threads 1
[2023-03-17 02:31:40,546] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:40,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:40,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:40,547] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:40,547] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:40,547] [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
--------------------------------------------------------------------------------
[2023-03-17 02:31:40,547] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6300/tc_result.tsv
[2023-03-17 02:31:40,547] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:40,547] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:40,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference/checkm_data
[2023-03-17 02:31:40,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:40,554] [INFO] Task started: CheckM
[2023-03-17 02:31:40,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6300/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6300/checkm_input OceanDNA-b6300/checkm_result
[2023-03-17 02:32:13,548] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:13,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 34.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:13,551] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:13,551] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:13,551] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6300/markers.fasta)
[2023-03-17 02:32:13,551] [INFO] Task started: Blastn
[2023-03-17 02:32:13,551] [INFO] Running command: blastn -query OceanDNA-b6300/markers.fasta -db /var/lib/cwl/stg65af3dab-768e-4aab-808f-19fc094866c7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6300/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:14,300] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:14,301] [INFO] Selected 24 target genomes.
[2023-03-17 02:32:14,302] [INFO] Target genome list was writen to OceanDNA-b6300/target_genomes_gtdb.txt
[2023-03-17 02:32:14,734] [INFO] Task started: fastANI
[2023-03-17 02:32:14,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg48f3eaa2-83ba-44a9-95c8-a376ce275791/OceanDNA-b6300.fa --refList OceanDNA-b6300/target_genomes_gtdb.txt --output OceanDNA-b6300/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:27,934] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:27,938] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:32:27,938] [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_013001285.1	s__SHLJ01 sp004283005	77.038	87	378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SHLJ01	95.0	99.69	99.59	0.94	0.91	6	-
GCA_013001965.1	s__SHLJ01 sp013001965	76.6368	82	378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SHLJ01	95.0	99.22	99.22	0.91	0.91	2	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.5894	51	378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.1255	63	378	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:27,938] [INFO] GTDB search result was written to OceanDNA-b6300/result_gtdb.tsv
[2023-03-17 02:32:27,939] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:27,939] [INFO] DFAST_QC result json was written to OceanDNA-b6300/dqc_result.json
[2023-03-17 02:32:27,939] [INFO] DFAST_QC completed!
[2023-03-17 02:32:27,939] [INFO] Total running time: 0h1m15s