[2023-03-16 11:24:21,872] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:24:21,873] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:24:21,873] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference
[2023-03-16 11:24:24,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:24:24,009] [INFO] Task started: Prodigal
[2023-03-16 11:24:24,010] [INFO] Running command: cat /var/lib/cwl/stg2d64cf1d-7b4f-45b4-9c43-7b9e4b9963dd/OceanDNA-b12631.fa | prodigal -d OceanDNA-b12631/cds.fna -a OceanDNA-b12631/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:24:45,075] [INFO] Task succeeded: Prodigal
[2023-03-16 11:24:45,075] [INFO] Task started: HMMsearch
[2023-03-16 11:24:45,075] [INFO] Running command: hmmsearch --tblout OceanDNA-b12631/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference/reference_markers.hmm OceanDNA-b12631/protein.faa > /dev/null
[2023-03-16 11:24:45,236] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:24:45,237] [INFO] Found 6/6 markers.
[2023-03-16 11:24:45,251] [INFO] Query marker FASTA was written to OceanDNA-b12631/markers.fasta
[2023-03-16 11:24:45,251] [INFO] Task started: Blastn
[2023-03-16 11:24:45,252] [INFO] Running command: blastn -query OceanDNA-b12631/markers.fasta -db /var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference/reference_markers.fasta -out OceanDNA-b12631/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:24:45,783] [INFO] Task succeeded: Blastn
[2023-03-16 11:24:45,784] [INFO] Selected 26 target genomes.
[2023-03-16 11:24:45,784] [INFO] Target genome list was writen to OceanDNA-b12631/target_genomes.txt
[2023-03-16 11:24:45,801] [INFO] Task started: fastANI
[2023-03-16 11:24:45,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d64cf1d-7b4f-45b4-9c43-7b9e4b9963dd/OceanDNA-b12631.fa --refList OceanDNA-b12631/target_genomes.txt --output OceanDNA-b12631/fastani_result.tsv --threads 1
[2023-03-16 11:25:00,105] [INFO] Task succeeded: fastANI
[2023-03-16 11:25:00,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:25:00,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:25:00,112] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:25:00,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:25:00,112] [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	77.0145	172	648	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	75.7469	50	648	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	75.6268	50	648	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	75.4285	51	648	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.3831	53	648	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	75.3671	52	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:25:00,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12631/tc_result.tsv
[2023-03-16 11:25:00,113] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:25:00,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:25:00,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference/checkm_data
[2023-03-16 11:25:00,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:25:00,118] [INFO] Task started: CheckM
[2023-03-16 11:25:00,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12631/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12631/checkm_input OceanDNA-b12631/checkm_result
[2023-03-16 11:25:33,515] [INFO] Task succeeded: CheckM
[2023-03-16 11:25:33,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:25:33,518] [INFO] ===== Completeness check finished =====
[2023-03-16 11:25:33,518] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:25:33,518] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12631/markers.fasta)
[2023-03-16 11:25:33,519] [INFO] Task started: Blastn
[2023-03-16 11:25:33,519] [INFO] Running command: blastn -query OceanDNA-b12631/markers.fasta -db /var/lib/cwl/stgbd3c7b57-2902-4519-9e13-e8b5dcd7cdc9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12631/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:25:34,270] [INFO] Task succeeded: Blastn
[2023-03-16 11:25:34,271] [INFO] Selected 15 target genomes.
[2023-03-16 11:25:34,271] [INFO] Target genome list was writen to OceanDNA-b12631/target_genomes_gtdb.txt
[2023-03-16 11:25:34,502] [INFO] Task started: fastANI
[2023-03-16 11:25:34,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d64cf1d-7b4f-45b4-9c43-7b9e4b9963dd/OceanDNA-b12631.fa --refList OceanDNA-b12631/target_genomes_gtdb.txt --output OceanDNA-b12631/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:25:42,316] [INFO] Task succeeded: fastANI
[2023-03-16 11:25:42,322] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:25:42,322] [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_905479915.1	s__GCA-002793235 sp905479915	79.1113	322	648	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_016763795.1	s__GCA-002793235 sp016763795	78.9638	331	648	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_002401955.1	s__GCA-002793235 sp002401955	78.8643	327	648	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_016763135.1	s__GCA-002793235 sp016763135	78.0065	231	648	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_002402165.1	s__GCA-002793235 sp002402165	77.9109	264	648	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_905479995.1	s__GCA-002793235 sp905479995	77.7609	184	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993035.1	s__Vicingus serpentipes	77.0145	172	648	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	76.8237	129	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__GCA-002793235	95.0	99.29	99.29	0.84	0.84	2	-
GCF_014062345.1	s__Tenacibaculum pelagium	75.6055	51	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:25:42,322] [INFO] GTDB search result was written to OceanDNA-b12631/result_gtdb.tsv
[2023-03-16 11:25:42,322] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:25:42,324] [INFO] DFAST_QC result json was written to OceanDNA-b12631/dqc_result.json
[2023-03-16 11:25:42,324] [INFO] DFAST_QC completed!
[2023-03-16 11:25:42,324] [INFO] Total running time: 0h1m20s