[2023-03-14 13:29:10,675] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:29:10,675] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:29:10,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference
[2023-03-14 13:29:11,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:29:11,837] [INFO] Task started: Prodigal
[2023-03-14 13:29:11,838] [INFO] Running command: cat /var/lib/cwl/stg19e998db-b0bb-4696-aabf-6bd18c078533/OceanDNA-b9587.fa | prodigal -d OceanDNA-b9587/cds.fna -a OceanDNA-b9587/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:29:32,346] [INFO] Task succeeded: Prodigal
[2023-03-14 13:29:32,346] [INFO] Task started: HMMsearch
[2023-03-14 13:29:32,346] [INFO] Running command: hmmsearch --tblout OceanDNA-b9587/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference/reference_markers.hmm OceanDNA-b9587/protein.faa > /dev/null
[2023-03-14 13:29:32,578] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:29:32,579] [INFO] Found 6/6 markers.
[2023-03-14 13:29:32,592] [INFO] Query marker FASTA was written to OceanDNA-b9587/markers.fasta
[2023-03-14 13:29:32,594] [INFO] Task started: Blastn
[2023-03-14 13:29:32,594] [INFO] Running command: blastn -query OceanDNA-b9587/markers.fasta -db /var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference/reference_markers.fasta -out OceanDNA-b9587/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:29:33,277] [INFO] Task succeeded: Blastn
[2023-03-14 13:29:33,278] [INFO] Selected 34 target genomes.
[2023-03-14 13:29:33,278] [INFO] Target genome list was writen to OceanDNA-b9587/target_genomes.txt
[2023-03-14 13:29:33,300] [INFO] Task started: fastANI
[2023-03-14 13:29:33,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e998db-b0bb-4696-aabf-6bd18c078533/OceanDNA-b9587.fa --refList OceanDNA-b9587/target_genomes.txt --output OceanDNA-b9587/fastani_result.tsv --threads 1
[2023-03-14 13:29:57,015] [INFO] Task succeeded: fastANI
[2023-03-14 13:29:57,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:29:57,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:29:57,016] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:29:57,016] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:29:57,016] [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
--------------------------------------------------------------------------------
[2023-03-14 13:29:57,016] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9587/tc_result.tsv
[2023-03-14 13:29:57,016] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:29:57,016] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:29:57,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference/checkm_data
[2023-03-14 13:29:57,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:29:57,023] [INFO] Task started: CheckM
[2023-03-14 13:29:57,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9587/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9587/checkm_input OceanDNA-b9587/checkm_result
[2023-03-14 13:30:38,292] [INFO] Task succeeded: CheckM
[2023-03-14 13:30:38,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:30:38,296] [INFO] ===== Completeness check finished =====
[2023-03-14 13:30:38,296] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:30:38,296] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9587/markers.fasta)
[2023-03-14 13:30:38,297] [INFO] Task started: Blastn
[2023-03-14 13:30:38,297] [INFO] Running command: blastn -query OceanDNA-b9587/markers.fasta -db /var/lib/cwl/stg3d2efd1c-ca82-4421-9d0d-6310e84a258d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9587/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:30:39,175] [INFO] Task succeeded: Blastn
[2023-03-14 13:30:39,177] [INFO] Selected 19 target genomes.
[2023-03-14 13:30:39,177] [INFO] Target genome list was writen to OceanDNA-b9587/target_genomes_gtdb.txt
[2023-03-14 13:30:39,193] [INFO] Task started: fastANI
[2023-03-14 13:30:39,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e998db-b0bb-4696-aabf-6bd18c078533/OceanDNA-b9587.fa --refList OceanDNA-b9587/target_genomes_gtdb.txt --output OceanDNA-b9587/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:30:46,107] [INFO] Task succeeded: fastANI
[2023-03-14 13:30:46,115] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:30:46,115] [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_017858055.1	s__MS024-2A sp002384715	99.7982	576	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	conclusive
GCA_017851655.1	s__MS024-2A sp017851655	79.009	273	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_902546725.1	s__MS024-2A sp902546725	78.0723	161	624	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_002167945.1	s__MS024-2A sp002167945	77.7475	172	624	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	77.4632	111	624	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_000173095.1	s__MS024-2A sp000173095	77.331	111	624	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	77.2538	128	624	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	77.0039	96	624	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	76.8533	105	624	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_905181615.1	s__UBA7428 sp905181615	76.3672	52	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_002714815.1	s__MS024-2A sp002714815	76.1478	76	624	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_003130815.1	s__MS024-2A sp003130815	76.1346	50	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:30:46,115] [INFO] GTDB search result was written to OceanDNA-b9587/result_gtdb.tsv
[2023-03-14 13:30:46,116] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:30:46,117] [INFO] DFAST_QC result json was written to OceanDNA-b9587/dqc_result.json
[2023-03-14 13:30:46,117] [INFO] DFAST_QC completed!
[2023-03-14 13:30:46,117] [INFO] Total running time: 0h1m35s