[2023-03-15 23:58:53,721] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:58:53,722] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:58:53,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference
[2023-03-15 23:58:54,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:58:54,832] [INFO] Task started: Prodigal
[2023-03-15 23:58:54,832] [INFO] Running command: cat /var/lib/cwl/stg02f80718-96e4-4275-b69d-3d02b19db11b/OceanDNA-b11319.fa | prodigal -d OceanDNA-b11319/cds.fna -a OceanDNA-b11319/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:59:06,033] [INFO] Task succeeded: Prodigal
[2023-03-15 23:59:06,034] [INFO] Task started: HMMsearch
[2023-03-15 23:59:06,034] [INFO] Running command: hmmsearch --tblout OceanDNA-b11319/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference/reference_markers.hmm OceanDNA-b11319/protein.faa > /dev/null
[2023-03-15 23:59:06,223] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:59:06,224] [INFO] Found 6/6 markers.
[2023-03-15 23:59:06,244] [INFO] Query marker FASTA was written to OceanDNA-b11319/markers.fasta
[2023-03-15 23:59:06,246] [INFO] Task started: Blastn
[2023-03-15 23:59:06,246] [INFO] Running command: blastn -query OceanDNA-b11319/markers.fasta -db /var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference/reference_markers.fasta -out OceanDNA-b11319/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:06,784] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:06,786] [INFO] Selected 35 target genomes.
[2023-03-15 23:59:06,786] [INFO] Target genome list was writen to OceanDNA-b11319/target_genomes.txt
[2023-03-15 23:59:06,803] [INFO] Task started: fastANI
[2023-03-15 23:59:06,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f80718-96e4-4275-b69d-3d02b19db11b/OceanDNA-b11319.fa --refList OceanDNA-b11319/target_genomes.txt --output OceanDNA-b11319/fastani_result.tsv --threads 1
[2023-03-15 23:59:24,496] [INFO] Task succeeded: fastANI
[2023-03-15 23:59:24,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:59:24,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:59:24,496] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:59:24,496] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:59:24,497] [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
--------------------------------------------------------------------------------
[2023-03-15 23:59:24,498] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11319/tc_result.tsv
[2023-03-15 23:59:24,500] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:59:24,500] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:59:24,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference/checkm_data
[2023-03-15 23:59:24,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:59:24,507] [INFO] Task started: CheckM
[2023-03-15 23:59:24,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11319/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11319/checkm_input OceanDNA-b11319/checkm_result
[2023-03-15 23:59:56,975] [INFO] Task succeeded: CheckM
[2023-03-15 23:59:56,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:59:57,037] [INFO] ===== Completeness check finished =====
[2023-03-15 23:59:57,037] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:59:57,037] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11319/markers.fasta)
[2023-03-15 23:59:57,038] [INFO] Task started: Blastn
[2023-03-15 23:59:57,038] [INFO] Running command: blastn -query OceanDNA-b11319/markers.fasta -db /var/lib/cwl/stg86c6d17f-b2e8-4f07-a0ff-4fea9858e4a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11319/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:59:57,772] [INFO] Task succeeded: Blastn
[2023-03-15 23:59:57,774] [INFO] Selected 21 target genomes.
[2023-03-15 23:59:57,775] [INFO] Target genome list was writen to OceanDNA-b11319/target_genomes_gtdb.txt
[2023-03-15 23:59:57,921] [INFO] Task started: fastANI
[2023-03-15 23:59:57,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg02f80718-96e4-4275-b69d-3d02b19db11b/OceanDNA-b11319.fa --refList OceanDNA-b11319/target_genomes_gtdb.txt --output OceanDNA-b11319/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:00:05,215] [INFO] Task succeeded: fastANI
[2023-03-16 00:00:05,220] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:00:05,221] [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_002716845.1	s__UBA8316 sp002716845	99.8199	380	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003538555.1	s__UBA8316 sp003538555	92.7792	289	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
GCA_002364535.1	s__UBA8316 sp002364535	77.7823	139	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002711215.1	s__UBA8316 sp002711215	77.727	89	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
GCA_018647605.1	s__UBA8316 sp018647605	77.1649	119	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619315.1	s__UBA8316 sp902619315	77.0624	76	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623955.1	s__UBA8316 sp018623955	76.8875	62	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	76.6923	117	497	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-16 00:00:05,222] [INFO] GTDB search result was written to OceanDNA-b11319/result_gtdb.tsv
[2023-03-16 00:00:05,222] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:00:05,224] [INFO] DFAST_QC result json was written to OceanDNA-b11319/dqc_result.json
[2023-03-16 00:00:05,224] [INFO] DFAST_QC completed!
[2023-03-16 00:00:05,224] [INFO] Total running time: 0h1m12s