[2023-03-16 21:45:13,164] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,164] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference
[2023-03-16 21:45:14,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:14,275] [INFO] Task started: Prodigal
[2023-03-16 21:45:14,275] [INFO] Running command: cat /var/lib/cwl/stg44c5ac69-9a84-4ea7-97ec-52d296c8fe7d/OceanDNA-b9447.fa | prodigal -d OceanDNA-b9447/cds.fna -a OceanDNA-b9447/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:22,495] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:22,495] [INFO] Task started: HMMsearch
[2023-03-16 21:45:22,496] [INFO] Running command: hmmsearch --tblout OceanDNA-b9447/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference/reference_markers.hmm OceanDNA-b9447/protein.faa > /dev/null
[2023-03-16 21:45:22,643] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:22,643] [INFO] Found 6/6 markers.
[2023-03-16 21:45:22,654] [INFO] Query marker FASTA was written to OceanDNA-b9447/markers.fasta
[2023-03-16 21:45:22,654] [INFO] Task started: Blastn
[2023-03-16 21:45:22,654] [INFO] Running command: blastn -query OceanDNA-b9447/markers.fasta -db /var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference/reference_markers.fasta -out OceanDNA-b9447/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:23,189] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:23,190] [INFO] Selected 28 target genomes.
[2023-03-16 21:45:23,190] [INFO] Target genome list was writen to OceanDNA-b9447/target_genomes.txt
[2023-03-16 21:45:23,202] [INFO] Task started: fastANI
[2023-03-16 21:45:23,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg44c5ac69-9a84-4ea7-97ec-52d296c8fe7d/OceanDNA-b9447.fa --refList OceanDNA-b9447/target_genomes.txt --output OceanDNA-b9447/fastani_result.tsv --threads 1
[2023-03-16 21:45:37,724] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:37,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:37,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:37,725] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:37,725] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:45:37,725] [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 21:45:37,726] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9447/tc_result.tsv
[2023-03-16 21:45:37,726] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:37,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:37,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference/checkm_data
[2023-03-16 21:45:37,729] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:37,731] [INFO] Task started: CheckM
[2023-03-16 21:45:37,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9447/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9447/checkm_input OceanDNA-b9447/checkm_result
[2023-03-16 21:46:03,594] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:03,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.06%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:03,596] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:03,596] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:03,596] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9447/markers.fasta)
[2023-03-16 21:46:03,596] [INFO] Task started: Blastn
[2023-03-16 21:46:03,597] [INFO] Running command: blastn -query OceanDNA-b9447/markers.fasta -db /var/lib/cwl/stg90fb1177-d845-4592-b5a9-22cdfd59c442/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9447/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:04,366] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:04,366] [INFO] Selected 9 target genomes.
[2023-03-16 21:46:04,366] [INFO] Target genome list was writen to OceanDNA-b9447/target_genomes_gtdb.txt
[2023-03-16 21:46:04,423] [INFO] Task started: fastANI
[2023-03-16 21:46:04,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg44c5ac69-9a84-4ea7-97ec-52d296c8fe7d/OceanDNA-b9447.fa --refList OceanDNA-b9447/target_genomes_gtdb.txt --output OceanDNA-b9447/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:07,078] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:07,083] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:07,084] [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_000173095.1	s__MS024-2A sp000173095	79.2988	220	364	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_009886625.1	s__MS024-2A sp009886625	78.7304	214	364	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_905181895.1	s__MS024-2A sp905181895	78.5079	136	364	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_905182305.1	s__MS024-2A sp905182305	77.0988	98	364	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_017852075.1	s__MS024-2A sp017852075	76.9723	57	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_002292265.1	s__MS024-2A sp002292265	76.5714	62	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.71	99.21	0.94	0.92	6	-
GCA_905480425.1	s__MS024-2A sp905480425	76.5251	92	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:07,084] [INFO] GTDB search result was written to OceanDNA-b9447/result_gtdb.tsv
[2023-03-16 21:46:07,084] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:07,085] [INFO] DFAST_QC result json was written to OceanDNA-b9447/dqc_result.json
[2023-03-16 21:46:07,085] [INFO] DFAST_QC completed!
[2023-03-16 21:46:07,085] [INFO] Total running time: 0h0m54s