[2023-03-18 21:18:16,436] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:18:16,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:18:16,436] [INFO] DQC Reference Directory: /var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference
[2023-03-18 21:18:17,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:18:17,549] [INFO] Task started: Prodigal
[2023-03-18 21:18:17,549] [INFO] Running command: cat /var/lib/cwl/stg4ca5afb2-a984-4b22-9682-cd997307586f/OceanDNA-b9541.fa | prodigal -d OceanDNA-b9541/cds.fna -a OceanDNA-b9541/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:18:29,488] [INFO] Task succeeded: Prodigal
[2023-03-18 21:18:29,488] [INFO] Task started: HMMsearch
[2023-03-18 21:18:29,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b9541/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference/reference_markers.hmm OceanDNA-b9541/protein.faa > /dev/null
[2023-03-18 21:18:29,673] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:18:29,674] [INFO] Found 6/6 markers.
[2023-03-18 21:18:29,688] [INFO] Query marker FASTA was written to OceanDNA-b9541/markers.fasta
[2023-03-18 21:18:29,689] [INFO] Task started: Blastn
[2023-03-18 21:18:29,689] [INFO] Running command: blastn -query OceanDNA-b9541/markers.fasta -db /var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference/reference_markers.fasta -out OceanDNA-b9541/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:18:30,293] [INFO] Task succeeded: Blastn
[2023-03-18 21:18:30,294] [INFO] Selected 35 target genomes.
[2023-03-18 21:18:30,294] [INFO] Target genome list was writen to OceanDNA-b9541/target_genomes.txt
[2023-03-18 21:18:30,323] [INFO] Task started: fastANI
[2023-03-18 21:18:30,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca5afb2-a984-4b22-9682-cd997307586f/OceanDNA-b9541.fa --refList OceanDNA-b9541/target_genomes.txt --output OceanDNA-b9541/fastani_result.tsv --threads 1
[2023-03-18 21:18:48,809] [INFO] Task succeeded: fastANI
[2023-03-18 21:18:48,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:18:48,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:18:48,810] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:18:48,810] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:18:48,810] [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
--------------------------------------------------------------------------------
[2023-03-18 21:18:48,811] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9541/tc_result.tsv
[2023-03-18 21:18:48,811] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:18:48,811] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:18:48,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference/checkm_data
[2023-03-18 21:18:48,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:18:48,876] [INFO] Task started: CheckM
[2023-03-18 21:18:48,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9541/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9541/checkm_input OceanDNA-b9541/checkm_result
[2023-03-18 21:19:23,110] [INFO] Task succeeded: CheckM
[2023-03-18 21:19:23,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:19:23,113] [INFO] ===== Completeness check finished =====
[2023-03-18 21:19:23,113] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:19:23,114] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9541/markers.fasta)
[2023-03-18 21:19:23,115] [INFO] Task started: Blastn
[2023-03-18 21:19:23,115] [INFO] Running command: blastn -query OceanDNA-b9541/markers.fasta -db /var/lib/cwl/stgd791582c-5805-49ff-9552-a99fd5d3df70/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9541/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:19:24,018] [INFO] Task succeeded: Blastn
[2023-03-18 21:19:24,019] [INFO] Selected 17 target genomes.
[2023-03-18 21:19:24,019] [INFO] Target genome list was writen to OceanDNA-b9541/target_genomes_gtdb.txt
[2023-03-18 21:19:24,034] [INFO] Task started: fastANI
[2023-03-18 21:19:24,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ca5afb2-a984-4b22-9682-cd997307586f/OceanDNA-b9541.fa --refList OceanDNA-b9541/target_genomes_gtdb.txt --output OceanDNA-b9541/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:19:30,145] [INFO] Task succeeded: fastANI
[2023-03-18 21:19:30,152] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:19:30,152] [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_002167945.1	s__MS024-2A sp002167945	96.6944	454	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902546725.1	s__MS024-2A sp902546725	90.5624	407	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525195.1	s__MS024-2A sp011525195	77.5378	147	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858055.1	s__MS024-2A sp002384715	77.4744	182	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
GCA_002705385.1	s__MS024-2A sp002705385	77.3932	135	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017851655.1	s__MS024-2A sp017851655	77.3622	190	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_905480425.1	s__MS024-2A sp905480425	76.8346	94	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_000173095.1	s__MS024-2A sp000173095	76.7395	113	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_008081175.1	s__MS024-2A sp008081175	76.4053	97	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.02	98.61	0.90	0.80	6	-
GCA_003130815.1	s__MS024-2A sp003130815	76.3647	54	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	76.2636	52	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:19:30,153] [INFO] GTDB search result was written to OceanDNA-b9541/result_gtdb.tsv
[2023-03-18 21:19:30,153] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:19:30,155] [INFO] DFAST_QC result json was written to OceanDNA-b9541/dqc_result.json
[2023-03-18 21:19:30,155] [INFO] DFAST_QC completed!
[2023-03-18 21:19:30,155] [INFO] Total running time: 0h1m14s