[2023-03-18 06:30:24,775] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,775] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,775] [INFO] DQC Reference Directory: /var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference
[2023-03-18 06:30:25,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,887] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,887] [INFO] Running command: cat /var/lib/cwl/stg46b1f986-b3b4-4a6f-8b30-1ae0b74c969e/OceanDNA-b30239.fa | prodigal -d OceanDNA-b30239/cds.fna -a OceanDNA-b30239/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:42,424] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:42,424] [INFO] Task started: HMMsearch
[2023-03-18 06:30:42,424] [INFO] Running command: hmmsearch --tblout OceanDNA-b30239/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference/reference_markers.hmm OceanDNA-b30239/protein.faa > /dev/null
[2023-03-18 06:30:42,618] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:42,618] [INFO] Found 6/6 markers.
[2023-03-18 06:30:42,638] [INFO] Query marker FASTA was written to OceanDNA-b30239/markers.fasta
[2023-03-18 06:30:42,638] [INFO] Task started: Blastn
[2023-03-18 06:30:42,638] [INFO] Running command: blastn -query OceanDNA-b30239/markers.fasta -db /var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference/reference_markers.fasta -out OceanDNA-b30239/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:43,294] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:43,295] [INFO] Selected 11 target genomes.
[2023-03-18 06:30:43,295] [INFO] Target genome list was writen to OceanDNA-b30239/target_genomes.txt
[2023-03-18 06:30:43,367] [INFO] Task started: fastANI
[2023-03-18 06:30:43,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg46b1f986-b3b4-4a6f-8b30-1ae0b74c969e/OceanDNA-b30239.fa --refList OceanDNA-b30239/target_genomes.txt --output OceanDNA-b30239/fastani_result.tsv --threads 1
[2023-03-18 06:30:51,192] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:51,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:51,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:51,200] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-18 06:30:51,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 06:30:51,200] [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
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	96.9118	841	866	95	conclusive
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	96.9111	823	866	95	conclusive
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	87.3466	763	866	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	84.0131	690	866	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	83.8984	606	866	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.5245	392	866	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.0327	231	866	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.6427	134	866	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.4438	191	866	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.358	169	866	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.358	169	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:30:51,206] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30239/tc_result.tsv
[2023-03-18 06:30:51,214] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:51,214] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:51,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference/checkm_data
[2023-03-18 06:30:51,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:51,221] [INFO] Task started: CheckM
[2023-03-18 06:30:51,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30239/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30239/checkm_input OceanDNA-b30239/checkm_result
[2023-03-18 06:31:34,461] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:34,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:34,534] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:34,534] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:34,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30239/markers.fasta)
[2023-03-18 06:31:34,535] [INFO] Task started: Blastn
[2023-03-18 06:31:34,535] [INFO] Running command: blastn -query OceanDNA-b30239/markers.fasta -db /var/lib/cwl/stgab5dc68f-f0f4-4236-a4ee-181f9b95d3cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30239/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:35,608] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:35,627] [INFO] Selected 7 target genomes.
[2023-03-18 06:31:35,627] [INFO] Target genome list was writen to OceanDNA-b30239/target_genomes_gtdb.txt
[2023-03-18 06:31:35,658] [INFO] Task started: fastANI
[2023-03-18 06:31:35,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg46b1f986-b3b4-4a6f-8b30-1ae0b74c969e/OceanDNA-b30239.fa --refList OceanDNA-b30239/target_genomes_gtdb.txt --output OceanDNA-b30239/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:40,980] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:40,985] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:31:40,985] [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_000172095.1	s__Sulfitobacter indolifex	96.9111	823	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003611275.1	s__Sulfitobacter sp001634775	87.5887	761	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_900113435.1	s__Sulfitobacter dubius	87.3466	763	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCA_002703405.1	s__Sulfitobacter sp002703405	86.6054	673	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_017743885.1	s__Sulfitobacter sp001635605	85.9896	735	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_900102535.1	s__Sulfitobacter delicatus	84.0411	688	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	83.8828	607	866	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:40,992] [INFO] GTDB search result was written to OceanDNA-b30239/result_gtdb.tsv
[2023-03-18 06:31:41,008] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:41,018] [INFO] DFAST_QC result json was written to OceanDNA-b30239/dqc_result.json
[2023-03-18 06:31:41,018] [INFO] DFAST_QC completed!
[2023-03-18 06:31:41,018] [INFO] Total running time: 0h1m16s