[2023-03-15 17:20:51,414] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:20:51,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:20:51,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference
[2023-03-15 17:20:52,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:20:52,527] [INFO] Task started: Prodigal
[2023-03-15 17:20:52,528] [INFO] Running command: cat /var/lib/cwl/stg2ee35aeb-52ae-4c44-b505-2afda691bfee/OceanDNA-b9455.fa | prodigal -d OceanDNA-b9455/cds.fna -a OceanDNA-b9455/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:21:06,332] [INFO] Task succeeded: Prodigal
[2023-03-15 17:21:06,333] [INFO] Task started: HMMsearch
[2023-03-15 17:21:06,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b9455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference/reference_markers.hmm OceanDNA-b9455/protein.faa > /dev/null
[2023-03-15 17:21:06,508] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:21:06,508] [INFO] Found 6/6 markers.
[2023-03-15 17:21:06,529] [INFO] Query marker FASTA was written to OceanDNA-b9455/markers.fasta
[2023-03-15 17:21:06,530] [INFO] Task started: Blastn
[2023-03-15 17:21:06,530] [INFO] Running command: blastn -query OceanDNA-b9455/markers.fasta -db /var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference/reference_markers.fasta -out OceanDNA-b9455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:21:07,097] [INFO] Task succeeded: Blastn
[2023-03-15 17:21:07,101] [INFO] Selected 25 target genomes.
[2023-03-15 17:21:07,101] [INFO] Target genome list was writen to OceanDNA-b9455/target_genomes.txt
[2023-03-15 17:21:07,115] [INFO] Task started: fastANI
[2023-03-15 17:21:07,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ee35aeb-52ae-4c44-b505-2afda691bfee/OceanDNA-b9455.fa --refList OceanDNA-b9455/target_genomes.txt --output OceanDNA-b9455/fastani_result.tsv --threads 1
[2023-03-15 17:21:21,516] [INFO] Task succeeded: fastANI
[2023-03-15 17:21:21,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:21:21,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:21:21,517] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:21:21,517] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:21:21,517] [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 17:21:21,519] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9455/tc_result.tsv
[2023-03-15 17:21:21,520] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:21:21,520] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:21:21,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference/checkm_data
[2023-03-15 17:21:21,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:21:21,588] [INFO] Task started: CheckM
[2023-03-15 17:21:21,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9455/checkm_input OceanDNA-b9455/checkm_result
[2023-03-15 17:22:00,187] [INFO] Task succeeded: CheckM
[2023-03-15 17:22:00,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:22:00,384] [INFO] ===== Completeness check finished =====
[2023-03-15 17:22:00,385] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:22:00,385] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9455/markers.fasta)
[2023-03-15 17:22:00,386] [INFO] Task started: Blastn
[2023-03-15 17:22:00,386] [INFO] Running command: blastn -query OceanDNA-b9455/markers.fasta -db /var/lib/cwl/stg9e21c7e9-a1bd-49c4-b81c-98cd99e65426/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:22:01,154] [INFO] Task succeeded: Blastn
[2023-03-15 17:22:01,159] [INFO] Selected 15 target genomes.
[2023-03-15 17:22:01,159] [INFO] Target genome list was writen to OceanDNA-b9455/target_genomes_gtdb.txt
[2023-03-15 17:22:01,213] [INFO] Task started: fastANI
[2023-03-15 17:22:01,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ee35aeb-52ae-4c44-b505-2afda691bfee/OceanDNA-b9455.fa --refList OceanDNA-b9455/target_genomes_gtdb.txt --output OceanDNA-b9455/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:22:07,716] [INFO] Task succeeded: fastANI
[2023-03-15 17:22:07,721] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:22:07,722] [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	80.1839	390	679	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	79.6396	376	679	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	79.4483	226	679	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_905480425.1	s__MS024-2A sp905480425	77.8177	182	679	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_905182305.1	s__MS024-2A sp905182305	77.7495	199	679	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_002292265.1	s__MS024-2A sp002292265	77.1687	130	679	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_017858055.1	s__MS024-2A sp002384715	77.0105	130	679	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_017852075.1	s__MS024-2A sp017852075	76.957	125	679	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-15 17:22:07,724] [INFO] GTDB search result was written to OceanDNA-b9455/result_gtdb.tsv
[2023-03-15 17:22:07,726] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:22:07,729] [INFO] DFAST_QC result json was written to OceanDNA-b9455/dqc_result.json
[2023-03-15 17:22:07,729] [INFO] DFAST_QC completed!
[2023-03-15 17:22:07,729] [INFO] Total running time: 0h1m16s