[2023-03-17 00:17:04,619] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference
[2023-03-17 00:17:05,816] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,817] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,817] [INFO] Running command: cat /var/lib/cwl/stgae087b6e-d5a2-4fe1-87db-c9aa4c0b6fe4/OceanDNA-b6232.fa | prodigal -d OceanDNA-b6232/cds.fna -a OceanDNA-b6232/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:17,027] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:17,028] [INFO] Task started: HMMsearch
[2023-03-17 00:17:17,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b6232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference/reference_markers.hmm OceanDNA-b6232/protein.faa > /dev/null
[2023-03-17 00:17:17,208] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:17,208] [INFO] Found 6/6 markers.
[2023-03-17 00:17:17,222] [INFO] Query marker FASTA was written to OceanDNA-b6232/markers.fasta
[2023-03-17 00:17:17,222] [INFO] Task started: Blastn
[2023-03-17 00:17:17,222] [INFO] Running command: blastn -query OceanDNA-b6232/markers.fasta -db /var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference/reference_markers.fasta -out OceanDNA-b6232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:17,762] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:17,763] [INFO] Selected 33 target genomes.
[2023-03-17 00:17:17,763] [INFO] Target genome list was writen to OceanDNA-b6232/target_genomes.txt
[2023-03-17 00:17:17,780] [INFO] Task started: fastANI
[2023-03-17 00:17:17,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgae087b6e-d5a2-4fe1-87db-c9aa4c0b6fe4/OceanDNA-b6232.fa --refList OceanDNA-b6232/target_genomes.txt --output OceanDNA-b6232/fastani_result.tsv --threads 1
[2023-03-17 00:17:36,182] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:36,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:36,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:36,183] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:36,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:17:36,183] [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 00:17:36,184] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6232/tc_result.tsv
[2023-03-17 00:17:36,184] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:36,184] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:36,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference/checkm_data
[2023-03-17 00:17:36,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:36,192] [INFO] Task started: CheckM
[2023-03-17 00:17:36,193] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6232/checkm_input OceanDNA-b6232/checkm_result
[2023-03-17 00:18:09,158] [INFO] Task succeeded: CheckM
[2023-03-17 00:18:09,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:18:09,252] [INFO] ===== Completeness check finished =====
[2023-03-17 00:18:09,252] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:18:09,253] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6232/markers.fasta)
[2023-03-17 00:18:09,253] [INFO] Task started: Blastn
[2023-03-17 00:18:09,253] [INFO] Running command: blastn -query OceanDNA-b6232/markers.fasta -db /var/lib/cwl/stgc35a098f-0734-4378-a295-2202bb0d8d97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:18:09,991] [INFO] Task succeeded: Blastn
[2023-03-17 00:18:09,992] [INFO] Selected 25 target genomes.
[2023-03-17 00:18:09,992] [INFO] Target genome list was writen to OceanDNA-b6232/target_genomes_gtdb.txt
[2023-03-17 00:18:10,094] [INFO] Task started: fastANI
[2023-03-17 00:18:10,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgae087b6e-d5a2-4fe1-87db-c9aa4c0b6fe4/OceanDNA-b6232.fa --refList OceanDNA-b6232/target_genomes_gtdb.txt --output OceanDNA-b6232/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:18:21,457] [INFO] Task succeeded: fastANI
[2023-03-17 00:18:21,462] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:18:21,462] [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_905182575.1	s__UBA8316 sp905182575	96.5835	459	523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	conclusive
GCA_017857815.1	s__UBA8316 sp017857815	92.5598	454	523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	77.1234	56	523	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_002364535.1	s__UBA8316 sp002364535	76.6593	55	523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_000173095.1	s__MS024-2A sp000173095	76.5127	62	523	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_018647605.1	s__UBA8316 sp018647605	76.3885	61	523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	76.0673	57	523	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:18:21,462] [INFO] GTDB search result was written to OceanDNA-b6232/result_gtdb.tsv
[2023-03-17 00:18:21,462] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:18:21,463] [INFO] DFAST_QC result json was written to OceanDNA-b6232/dqc_result.json
[2023-03-17 00:18:21,463] [INFO] DFAST_QC completed!
[2023-03-17 00:18:21,463] [INFO] Total running time: 0h1m17s