[2023-03-15 14:29:50,625] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:50,626] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:50,626] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference
[2023-03-15 14:29:51,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:51,711] [INFO] Task started: Prodigal
[2023-03-15 14:29:51,711] [INFO] Running command: cat /var/lib/cwl/stg6bc09bfb-9a76-495b-8cfb-e20ecee91265/OceanDNA-b12619.fa | prodigal -d OceanDNA-b12619/cds.fna -a OceanDNA-b12619/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:30:02,482] [INFO] Task succeeded: Prodigal
[2023-03-15 14:30:02,483] [INFO] Task started: HMMsearch
[2023-03-15 14:30:02,483] [INFO] Running command: hmmsearch --tblout OceanDNA-b12619/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference/reference_markers.hmm OceanDNA-b12619/protein.faa > /dev/null
[2023-03-15 14:30:02,680] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:30:02,680] [INFO] Found 6/6 markers.
[2023-03-15 14:30:02,697] [INFO] Query marker FASTA was written to OceanDNA-b12619/markers.fasta
[2023-03-15 14:30:02,699] [INFO] Task started: Blastn
[2023-03-15 14:30:02,699] [INFO] Running command: blastn -query OceanDNA-b12619/markers.fasta -db /var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference/reference_markers.fasta -out OceanDNA-b12619/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:03,226] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:03,232] [INFO] Selected 25 target genomes.
[2023-03-15 14:30:03,232] [INFO] Target genome list was writen to OceanDNA-b12619/target_genomes.txt
[2023-03-15 14:30:03,248] [INFO] Task started: fastANI
[2023-03-15 14:30:03,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc09bfb-9a76-495b-8cfb-e20ecee91265/OceanDNA-b12619.fa --refList OceanDNA-b12619/target_genomes.txt --output OceanDNA-b12619/fastani_result.tsv --threads 1
[2023-03-15 14:30:16,498] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:16,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:30:16,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:30:16,502] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:30:16,502] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:30:16,502] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	76.6807	102	490	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:30:16,519] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12619/tc_result.tsv
[2023-03-15 14:30:16,526] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:30:16,527] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:30:16,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference/checkm_data
[2023-03-15 14:30:16,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:30:16,532] [INFO] Task started: CheckM
[2023-03-15 14:30:16,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12619/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12619/checkm_input OceanDNA-b12619/checkm_result
[2023-03-15 14:30:48,579] [INFO] Task succeeded: CheckM
[2023-03-15 14:30:48,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:30:48,587] [INFO] ===== Completeness check finished =====
[2023-03-15 14:30:48,587] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:30:48,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12619/markers.fasta)
[2023-03-15 14:30:48,587] [INFO] Task started: Blastn
[2023-03-15 14:30:48,587] [INFO] Running command: blastn -query OceanDNA-b12619/markers.fasta -db /var/lib/cwl/stgf5fd99e2-5418-40ff-9193-3ba38ba34649/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12619/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:30:49,393] [INFO] Task succeeded: Blastn
[2023-03-15 14:30:49,393] [INFO] Selected 11 target genomes.
[2023-03-15 14:30:49,393] [INFO] Target genome list was writen to OceanDNA-b12619/target_genomes_gtdb.txt
[2023-03-15 14:30:49,430] [INFO] Task started: fastANI
[2023-03-15 14:30:49,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bc09bfb-9a76-495b-8cfb-e20ecee91265/OceanDNA-b12619.fa --refList OceanDNA-b12619/target_genomes_gtdb.txt --output OceanDNA-b12619/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:30:55,504] [INFO] Task succeeded: fastANI
[2023-03-15 14:30:55,510] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:30:55,510] [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_000961845.1	s__BRH-c54 sp000961845	94.7464	413	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359215.1	s__BRH-c54 sp002359215	93.27	440	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	98.22	0.97	0.91	4	-
GCA_002841035.1	s__BRH-c54 sp002841035	80.2962	189	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002770955.1	s__BRH-c54 sp002770955	79.6584	220	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__BRH-c54	95.0	99.41	99.41	0.88	0.88	2	-
GCF_007993035.1	s__Vicingus serpentipes	76.6807	102	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002790175.1	s__GCA-002793235 sp002790175	76.6177	84	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	99.29	99.29	0.84	0.84	2	-
GCA_905479995.1	s__GCA-002793235 sp905479995	76.5417	80	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183805.1	s__Vicingus sp016183805	76.5186	98	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__Vicingus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763135.1	s__GCA-002793235 sp016763135	75.8193	55	490	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:30:55,510] [INFO] GTDB search result was written to OceanDNA-b12619/result_gtdb.tsv
[2023-03-15 14:30:55,510] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:30:55,511] [INFO] DFAST_QC result json was written to OceanDNA-b12619/dqc_result.json
[2023-03-15 14:30:55,511] [INFO] DFAST_QC completed!
[2023-03-15 14:30:55,511] [INFO] Total running time: 0h1m5s