[2023-03-18 00:21:54,210] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,210] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference
[2023-03-18 00:21:55,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,651] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stg6ee042fb-6eef-4d34-998d-840e8b78be4d/OceanDNA-b6675.fa | prodigal -d OceanDNA-b6675/cds.fna -a OceanDNA-b6675/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:03,597] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:03,597] [INFO] Task started: HMMsearch
[2023-03-18 00:22:03,597] [INFO] Running command: hmmsearch --tblout OceanDNA-b6675/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference/reference_markers.hmm OceanDNA-b6675/protein.faa > /dev/null
[2023-03-18 00:22:03,752] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:03,753] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6ee042fb-6eef-4d34-998d-840e8b78be4d/OceanDNA-b6675.fa]
[2023-03-18 00:22:03,768] [INFO] Query marker FASTA was written to OceanDNA-b6675/markers.fasta
[2023-03-18 00:22:03,768] [INFO] Task started: Blastn
[2023-03-18 00:22:03,768] [INFO] Running command: blastn -query OceanDNA-b6675/markers.fasta -db /var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference/reference_markers.fasta -out OceanDNA-b6675/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:04,258] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:04,258] [INFO] Selected 14 target genomes.
[2023-03-18 00:22:04,259] [INFO] Target genome list was writen to OceanDNA-b6675/target_genomes.txt
[2023-03-18 00:22:04,268] [INFO] Task started: fastANI
[2023-03-18 00:22:04,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ee042fb-6eef-4d34-998d-840e8b78be4d/OceanDNA-b6675.fa --refList OceanDNA-b6675/target_genomes.txt --output OceanDNA-b6675/fastani_result.tsv --threads 1
[2023-03-18 00:22:12,474] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:12,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:12,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:12,480] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 00:22:12,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 00:22:12,481] [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
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	96.6823	217	233	95	conclusive
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	78.674	105	233	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	78.6355	112	233	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	77.2367	51	233	95	below_threshold
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	77.0354	53	233	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.9461	55	233	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:22:12,481] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6675/tc_result.tsv
[2023-03-18 00:22:12,481] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:12,481] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:12,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference/checkm_data
[2023-03-18 00:22:12,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:12,485] [INFO] Task started: CheckM
[2023-03-18 00:22:12,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6675/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6675/checkm_input OceanDNA-b6675/checkm_result
[2023-03-18 00:22:37,551] [INFO] Task succeeded: CheckM
[2023-03-18 00:22:37,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:22:37,554] [INFO] ===== Completeness check finished =====
[2023-03-18 00:22:37,554] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:22:37,554] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6675/markers.fasta)
[2023-03-18 00:22:37,554] [INFO] Task started: Blastn
[2023-03-18 00:22:37,554] [INFO] Running command: blastn -query OceanDNA-b6675/markers.fasta -db /var/lib/cwl/stg52922249-2063-4546-b2fd-b1907ca0e05f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6675/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:38,172] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:38,173] [INFO] Selected 11 target genomes.
[2023-03-18 00:22:38,173] [INFO] Target genome list was writen to OceanDNA-b6675/target_genomes_gtdb.txt
[2023-03-18 00:22:38,186] [INFO] Task started: fastANI
[2023-03-18 00:22:38,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ee042fb-6eef-4d34-998d-840e8b78be4d/OceanDNA-b6675.fa --refList OceanDNA-b6675/target_genomes_gtdb.txt --output OceanDNA-b6675/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:22:45,271] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:45,278] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:22:45,278] [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
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	96.6823	217	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009797025.1	s__Cellulophaga sp009797025	78.747	97	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	78.7145	104	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_000186265.1	s__Cellulophaga algicola	78.6355	112	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_018861125.1	s__Cellulophaga baltica_A	78.5696	83	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	78.4512	108	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799565.1	s__Cellulophaga sp000799565	77.7001	91	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	77.2367	51	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	77.0354	53	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_900119145.1	s__Cellulophaga fucicola	76.9461	55	233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:22:45,278] [INFO] GTDB search result was written to OceanDNA-b6675/result_gtdb.tsv
[2023-03-18 00:22:45,278] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:22:45,279] [INFO] DFAST_QC result json was written to OceanDNA-b6675/dqc_result.json
[2023-03-18 00:22:45,280] [INFO] DFAST_QC completed!
[2023-03-18 00:22:45,280] [INFO] Total running time: 0h0m51s