[2023-03-15 04:45:50,554] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:45:50,555] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:45:50,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference
[2023-03-15 04:45:51,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:45:51,674] [INFO] Task started: Prodigal
[2023-03-15 04:45:51,675] [INFO] Running command: cat /var/lib/cwl/stg81b6c6bb-6d72-4c5c-828f-d7780cc09af6/OceanDNA-b36666.fa | prodigal -d OceanDNA-b36666/cds.fna -a OceanDNA-b36666/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:46:19,206] [INFO] Task succeeded: Prodigal
[2023-03-15 04:46:19,206] [INFO] Task started: HMMsearch
[2023-03-15 04:46:19,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b36666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference/reference_markers.hmm OceanDNA-b36666/protein.faa > /dev/null
[2023-03-15 04:46:19,433] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:46:19,434] [INFO] Found 6/6 markers.
[2023-03-15 04:46:19,475] [INFO] Query marker FASTA was written to OceanDNA-b36666/markers.fasta
[2023-03-15 04:46:19,476] [INFO] Task started: Blastn
[2023-03-15 04:46:19,476] [INFO] Running command: blastn -query OceanDNA-b36666/markers.fasta -db /var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference/reference_markers.fasta -out OceanDNA-b36666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:46:20,117] [INFO] Task succeeded: Blastn
[2023-03-15 04:46:20,129] [INFO] Selected 28 target genomes.
[2023-03-15 04:46:20,129] [INFO] Target genome list was writen to OceanDNA-b36666/target_genomes.txt
[2023-03-15 04:46:20,146] [INFO] Task started: fastANI
[2023-03-15 04:46:20,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg81b6c6bb-6d72-4c5c-828f-d7780cc09af6/OceanDNA-b36666.fa --refList OceanDNA-b36666/target_genomes.txt --output OceanDNA-b36666/fastani_result.tsv --threads 1
[2023-03-15 04:46:38,311] [INFO] Task succeeded: fastANI
[2023-03-15 04:46:38,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:46:38,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:46:38,316] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:46:38,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:46:38,317] [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
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	78.0345	261	1521	95	below_threshold
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	77.6055	305	1521	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	77.351	181	1521	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.7876	52	1521	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:46:38,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36666/tc_result.tsv
[2023-03-15 04:46:38,323] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:46:38,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:46:38,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference/checkm_data
[2023-03-15 04:46:38,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:46:38,334] [INFO] Task started: CheckM
[2023-03-15 04:46:38,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36666/checkm_input OceanDNA-b36666/checkm_result
[2023-03-15 04:47:45,589] [INFO] Task succeeded: CheckM
[2023-03-15 04:47:45,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:47:45,713] [INFO] ===== Completeness check finished =====
[2023-03-15 04:47:45,713] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:47:45,713] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36666/markers.fasta)
[2023-03-15 04:47:45,714] [INFO] Task started: Blastn
[2023-03-15 04:47:45,714] [INFO] Running command: blastn -query OceanDNA-b36666/markers.fasta -db /var/lib/cwl/stg28e632b6-a778-4aba-a321-62979f95bb0a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:47:46,802] [INFO] Task succeeded: Blastn
[2023-03-15 04:47:46,818] [INFO] Selected 8 target genomes.
[2023-03-15 04:47:46,819] [INFO] Target genome list was writen to OceanDNA-b36666/target_genomes_gtdb.txt
[2023-03-15 04:47:46,827] [INFO] Task started: fastANI
[2023-03-15 04:47:46,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg81b6c6bb-6d72-4c5c-828f-d7780cc09af6/OceanDNA-b36666.fa --refList OceanDNA-b36666/target_genomes_gtdb.txt --output OceanDNA-b36666/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:47:54,777] [INFO] Task succeeded: fastANI
[2023-03-15 04:47:54,783] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:47:54,783] [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_000953825.1	s__Cellvibrio sp000953825	93.1344	1217	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	81.4925	944	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003524365.1	s__Cellvibrio sp003524365	81.405	788	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858205.1	s__Cellvibrio sp903858205	80.9375	650	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363885.1	s__Cellvibrio sp004363885	80.5596	751	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	79.754	676	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_002007605.1	s__Cellvibrio sp002007605	79.5584	626	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_001183545.1	s__Cellvibrio sp001183545	79.4055	704	1521	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:47:54,788] [INFO] GTDB search result was written to OceanDNA-b36666/result_gtdb.tsv
[2023-03-15 04:47:54,793] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:47:54,799] [INFO] DFAST_QC result json was written to OceanDNA-b36666/dqc_result.json
[2023-03-15 04:47:54,799] [INFO] DFAST_QC completed!
[2023-03-15 04:47:54,799] [INFO] Total running time: 0h2m4s