[2023-03-15 15:51:29,970] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stgf1519276-ff2c-4778-a044-e9406561f0d0/OceanDNA-b36668.fa | prodigal -d OceanDNA-b36668/cds.fna -a OceanDNA-b36668/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:45,072] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:45,073] [INFO] Task started: HMMsearch
[2023-03-15 15:51:45,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b36668/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference/reference_markers.hmm OceanDNA-b36668/protein.faa > /dev/null
[2023-03-15 15:51:45,306] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:45,307] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf1519276-ff2c-4778-a044-e9406561f0d0/OceanDNA-b36668.fa]
[2023-03-15 15:51:45,326] [INFO] Query marker FASTA was written to OceanDNA-b36668/markers.fasta
[2023-03-15 15:51:45,327] [INFO] Task started: Blastn
[2023-03-15 15:51:45,327] [INFO] Running command: blastn -query OceanDNA-b36668/markers.fasta -db /var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference/reference_markers.fasta -out OceanDNA-b36668/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:45,864] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:45,865] [INFO] Selected 22 target genomes.
[2023-03-15 15:51:45,865] [INFO] Target genome list was writen to OceanDNA-b36668/target_genomes.txt
[2023-03-15 15:51:45,876] [INFO] Task started: fastANI
[2023-03-15 15:51:45,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1519276-ff2c-4778-a044-e9406561f0d0/OceanDNA-b36668.fa --refList OceanDNA-b36668/target_genomes.txt --output OceanDNA-b36668/fastani_result.tsv --threads 1
[2023-03-15 15:51:59,720] [INFO] Task succeeded: fastANI
[2023-03-15 15:51:59,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:51:59,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:51:59,725] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:51:59,725] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:51:59,725] [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 japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	77.2376	163	760	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	76.8637	118	760	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.6712	71	760	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:51:59,726] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36668/tc_result.tsv
[2023-03-15 15:51:59,726] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:51:59,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:51:59,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference/checkm_data
[2023-03-15 15:51:59,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:51:59,731] [INFO] Task started: CheckM
[2023-03-15 15:51:59,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36668/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36668/checkm_input OceanDNA-b36668/checkm_result
[2023-03-15 15:52:36,535] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:36,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:36,537] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:36,538] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:36,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36668/markers.fasta)
[2023-03-15 15:52:36,538] [INFO] Task started: Blastn
[2023-03-15 15:52:36,538] [INFO] Running command: blastn -query OceanDNA-b36668/markers.fasta -db /var/lib/cwl/stg2e7b4c76-8aa6-47b9-9521-afe10ef45688/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36668/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:37,284] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:37,285] [INFO] Selected 14 target genomes.
[2023-03-15 15:52:37,285] [INFO] Target genome list was writen to OceanDNA-b36668/target_genomes_gtdb.txt
[2023-03-15 15:52:37,298] [INFO] Task started: fastANI
[2023-03-15 15:52:37,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1519276-ff2c-4778-a044-e9406561f0d0/OceanDNA-b36668.fa --refList OceanDNA-b36668/target_genomes_gtdb.txt --output OceanDNA-b36668/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:52:48,302] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:48,309] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:52:48,309] [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_004363885.1	s__Cellvibrio sp004363885	80.2009	435	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	79.7562	406	760	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	79.6492	413	760	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	79.3902	304	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001183545.1	s__Cellvibrio sp001183545	78.9735	351	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483365.1	s__Cellvibrio sp002483365	78.6671	340	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007605.1	s__Cellvibrio sp002007605	78.6264	328	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_008806955.1	s__Cellvibrio sp000263355	78.5259	332	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_008806975.1	s__Cellvibrio sp008806975	78.3133	297	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766945.1	s__Cellvibrio mixtus_A	78.0433	290	760	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712405.1	s__Cellvibrio sp016712405	76.6899	90	760	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 15:52:48,309] [INFO] GTDB search result was written to OceanDNA-b36668/result_gtdb.tsv
[2023-03-15 15:52:48,309] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:52:48,311] [INFO] DFAST_QC result json was written to OceanDNA-b36668/dqc_result.json
[2023-03-15 15:52:48,311] [INFO] DFAST_QC completed!
[2023-03-15 15:52:48,311] [INFO] Total running time: 0h1m18s