[2023-03-15 20:34:26,739] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference
[2023-03-15 20:34:28,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,460] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,460] [INFO] Running command: cat /var/lib/cwl/stgfc7fb087-e6c8-4724-8601-a0492e65dbc7/OceanDNA-b10940.fa | prodigal -d OceanDNA-b10940/cds.fna -a OceanDNA-b10940/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:40,701] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:40,701] [INFO] Task started: HMMsearch
[2023-03-15 20:34:40,701] [INFO] Running command: hmmsearch --tblout OceanDNA-b10940/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference/reference_markers.hmm OceanDNA-b10940/protein.faa > /dev/null
[2023-03-15 20:34:40,873] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:40,874] [INFO] Found 6/6 markers.
[2023-03-15 20:34:40,886] [INFO] Query marker FASTA was written to OceanDNA-b10940/markers.fasta
[2023-03-15 20:34:40,887] [INFO] Task started: Blastn
[2023-03-15 20:34:40,887] [INFO] Running command: blastn -query OceanDNA-b10940/markers.fasta -db /var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference/reference_markers.fasta -out OceanDNA-b10940/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:41,431] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:41,432] [INFO] Selected 39 target genomes.
[2023-03-15 20:34:41,433] [INFO] Target genome list was writen to OceanDNA-b10940/target_genomes.txt
[2023-03-15 20:34:41,454] [INFO] Task started: fastANI
[2023-03-15 20:34:41,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7fb087-e6c8-4724-8601-a0492e65dbc7/OceanDNA-b10940.fa --refList OceanDNA-b10940/target_genomes.txt --output OceanDNA-b10940/fastani_result.tsv --threads 1
[2023-03-15 20:35:02,764] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:02,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:35:02,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:35:02,764] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:35:02,765] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:35:02,765] [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 20:35:02,765] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10940/tc_result.tsv
[2023-03-15 20:35:02,765] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:35:02,765] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:35:02,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference/checkm_data
[2023-03-15 20:35:02,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:35:02,771] [INFO] Task started: CheckM
[2023-03-15 20:35:02,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10940/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10940/checkm_input OceanDNA-b10940/checkm_result
[2023-03-15 20:35:37,625] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:37,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.21%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:37,627] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:37,627] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:37,627] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10940/markers.fasta)
[2023-03-15 20:35:37,628] [INFO] Task started: Blastn
[2023-03-15 20:35:37,628] [INFO] Running command: blastn -query OceanDNA-b10940/markers.fasta -db /var/lib/cwl/stg32709884-076a-4fc6-90f0-a4456f57092a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10940/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:38,366] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:38,367] [INFO] Selected 27 target genomes.
[2023-03-15 20:35:38,367] [INFO] Target genome list was writen to OceanDNA-b10940/target_genomes_gtdb.txt
[2023-03-15 20:35:38,924] [INFO] Task started: fastANI
[2023-03-15 20:35:38,925] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7fb087-e6c8-4724-8601-a0492e65dbc7/OceanDNA-b10940.fa --refList OceanDNA-b10940/target_genomes_gtdb.txt --output OceanDNA-b10940/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:50,622] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:50,628] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 20:35:50,628] [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_905478905.1	s__UBA7428 sp905478905	98.8469	425	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	conclusive
GCA_002477625.1	s__UBA7428 sp002477625	76.9443	55	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_011526285.1	s__UBA7428 sp011526285	76.8589	134	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608425.1	s__UBA7428 sp018608425	76.7319	51	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526275.1	s__UBA7428 sp011526275	76.5843	118	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526265.1	s__UBA7428 sp011526265	76.2954	83	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	76.1368	74	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_011526335.1	s__UBA7428 sp011526335	76.1363	63	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708445.1	s__UBA7428 sp002708445	75.8359	64	540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:50,628] [INFO] GTDB search result was written to OceanDNA-b10940/result_gtdb.tsv
[2023-03-15 20:35:50,629] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:50,629] [INFO] DFAST_QC result json was written to OceanDNA-b10940/dqc_result.json
[2023-03-15 20:35:50,629] [INFO] DFAST_QC completed!
[2023-03-15 20:35:50,630] [INFO] Total running time: 0h1m24s