[2023-03-17 11:13:09,379] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:13:09,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:13:09,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference
[2023-03-17 11:13:11,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:13:11,243] [INFO] Task started: Prodigal
[2023-03-17 11:13:11,243] [INFO] Running command: cat /var/lib/cwl/stgedb73ea8-08d3-4bcd-9e70-043802ec59f0/OceanDNA-b30237.fa | prodigal -d OceanDNA-b30237/cds.fna -a OceanDNA-b30237/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:13:27,325] [INFO] Task succeeded: Prodigal
[2023-03-17 11:13:27,326] [INFO] Task started: HMMsearch
[2023-03-17 11:13:27,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b30237/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference/reference_markers.hmm OceanDNA-b30237/protein.faa > /dev/null
[2023-03-17 11:13:27,510] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:13:27,511] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgedb73ea8-08d3-4bcd-9e70-043802ec59f0/OceanDNA-b30237.fa]
[2023-03-17 11:13:27,528] [INFO] Query marker FASTA was written to OceanDNA-b30237/markers.fasta
[2023-03-17 11:13:27,530] [INFO] Task started: Blastn
[2023-03-17 11:13:27,530] [INFO] Running command: blastn -query OceanDNA-b30237/markers.fasta -db /var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference/reference_markers.fasta -out OceanDNA-b30237/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:13:28,274] [INFO] Task succeeded: Blastn
[2023-03-17 11:13:28,274] [INFO] Selected 12 target genomes.
[2023-03-17 11:13:28,275] [INFO] Target genome list was writen to OceanDNA-b30237/target_genomes.txt
[2023-03-17 11:13:28,289] [INFO] Task started: fastANI
[2023-03-17 11:13:28,289] [INFO] Running command: fastANI --query /var/lib/cwl/stgedb73ea8-08d3-4bcd-9e70-043802ec59f0/OceanDNA-b30237.fa --refList OceanDNA-b30237/target_genomes.txt --output OceanDNA-b30237/fastani_result.tsv --threads 1
[2023-03-17 11:13:37,001] [INFO] Task succeeded: fastANI
[2023-03-17 11:13:37,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:13:37,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:13:37,020] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 11:13:37,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 11:13:37,020] [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 delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	96.6995	782	845	95	conclusive
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	84.4981	612	845	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	83.5733	583	845	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	83.3993	603	845	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	83.3946	587	845	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.6209	335	845	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.0476	216	845	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.9018	195	845	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.8065	179	845	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.7238	184	845	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.6313	183	845	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.6014	132	845	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:13:37,020] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30237/tc_result.tsv
[2023-03-17 11:13:37,020] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:13:37,020] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:13:37,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference/checkm_data
[2023-03-17 11:13:37,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:13:37,046] [INFO] Task started: CheckM
[2023-03-17 11:13:37,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30237/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30237/checkm_input OceanDNA-b30237/checkm_result
[2023-03-17 11:14:19,271] [INFO] Task succeeded: CheckM
[2023-03-17 11:14:19,271] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:14:19,275] [INFO] ===== Completeness check finished =====
[2023-03-17 11:14:19,275] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:14:19,275] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30237/markers.fasta)
[2023-03-17 11:14:19,277] [INFO] Task started: Blastn
[2023-03-17 11:14:19,277] [INFO] Running command: blastn -query OceanDNA-b30237/markers.fasta -db /var/lib/cwl/stg98592208-d755-44c3-9514-51f38be73855/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30237/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:14:20,668] [INFO] Task succeeded: Blastn
[2023-03-17 11:14:20,668] [INFO] Selected 10 target genomes.
[2023-03-17 11:14:20,668] [INFO] Target genome list was writen to OceanDNA-b30237/target_genomes_gtdb.txt
[2023-03-17 11:14:20,681] [INFO] Task started: fastANI
[2023-03-17 11:14:20,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgedb73ea8-08d3-4bcd-9e70-043802ec59f0/OceanDNA-b30237.fa --refList OceanDNA-b30237/target_genomes_gtdb.txt --output OceanDNA-b30237/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:14:27,978] [INFO] Task succeeded: fastANI
[2023-03-17 11:14:27,984] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:14:27,985] [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_900102535.1	s__Sulfitobacter delicatus	96.6995	782	845	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_013346665.1	s__Sulfitobacter maritimus	84.5058	611	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	83.7535	621	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_017743885.1	s__Sulfitobacter sp001635605	83.7042	627	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_900113435.1	s__Sulfitobacter dubius	83.5733	583	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_000172095.1	s__Sulfitobacter indolifex	83.3983	586	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703405.1	s__Sulfitobacter sp002703405	83.0357	553	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_001634885.1	s__Sulfitobacter sp001634885	78.3644	279	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	77.6209	335	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	77.0476	216	845	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:14:27,985] [INFO] GTDB search result was written to OceanDNA-b30237/result_gtdb.tsv
[2023-03-17 11:14:27,985] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:14:27,986] [INFO] DFAST_QC result json was written to OceanDNA-b30237/dqc_result.json
[2023-03-17 11:14:27,986] [INFO] DFAST_QC completed!
[2023-03-17 11:14:27,986] [INFO] Total running time: 0h1m19s