[2023-03-19 03:14:58,371] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:14:58,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:14:58,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference
[2023-03-19 03:14:59,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:14:59,441] [INFO] Task started: Prodigal
[2023-03-19 03:14:59,441] [INFO] Running command: cat /var/lib/cwl/stgeeb0f25a-c231-4b21-803d-2c5ea87f0433/OceanDNA-b30238.fa | prodigal -d OceanDNA-b30238/cds.fna -a OceanDNA-b30238/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:15:21,070] [INFO] Task succeeded: Prodigal
[2023-03-19 03:15:21,071] [INFO] Task started: HMMsearch
[2023-03-19 03:15:21,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b30238/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference/reference_markers.hmm OceanDNA-b30238/protein.faa > /dev/null
[2023-03-19 03:15:21,272] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:15:21,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeeb0f25a-c231-4b21-803d-2c5ea87f0433/OceanDNA-b30238.fa]
[2023-03-19 03:15:21,296] [INFO] Query marker FASTA was written to OceanDNA-b30238/markers.fasta
[2023-03-19 03:15:21,298] [INFO] Task started: Blastn
[2023-03-19 03:15:21,298] [INFO] Running command: blastn -query OceanDNA-b30238/markers.fasta -db /var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference/reference_markers.fasta -out OceanDNA-b30238/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:15:21,947] [INFO] Task succeeded: Blastn
[2023-03-19 03:15:21,947] [INFO] Selected 11 target genomes.
[2023-03-19 03:15:21,948] [INFO] Target genome list was writen to OceanDNA-b30238/target_genomes.txt
[2023-03-19 03:15:21,953] [INFO] Task started: fastANI
[2023-03-19 03:15:21,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb0f25a-c231-4b21-803d-2c5ea87f0433/OceanDNA-b30238.fa --refList OceanDNA-b30238/target_genomes.txt --output OceanDNA-b30238/fastani_result.tsv --threads 1
[2023-03-19 03:15:30,331] [INFO] Task succeeded: fastANI
[2023-03-19 03:15:30,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:15:30,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:15:30,339] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 03:15:30,339] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 03:15:30,339] [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 dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	97.7837	1039	1119	95	conclusive
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	87.3911	909	1119	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	87.3655	944	1119	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	84.4317	811	1119	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	83.9668	762	1119	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.2776	284	1119	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.2258	284	1119	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2132	242	1119	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.7737	143	1119	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7686	153	1119	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.5615	242	1119	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:15:30,340] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30238/tc_result.tsv
[2023-03-19 03:15:30,341] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:15:30,342] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:15:30,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference/checkm_data
[2023-03-19 03:15:30,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:15:30,348] [INFO] Task started: CheckM
[2023-03-19 03:15:30,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30238/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30238/checkm_input OceanDNA-b30238/checkm_result
[2023-03-19 03:16:24,397] [INFO] Task succeeded: CheckM
[2023-03-19 03:16:24,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:16:24,417] [INFO] ===== Completeness check finished =====
[2023-03-19 03:16:24,417] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:16:24,418] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30238/markers.fasta)
[2023-03-19 03:16:24,418] [INFO] Task started: Blastn
[2023-03-19 03:16:24,418] [INFO] Running command: blastn -query OceanDNA-b30238/markers.fasta -db /var/lib/cwl/stg402be8db-3c11-4ca7-967e-e697a334b061/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30238/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:16:25,430] [INFO] Task succeeded: Blastn
[2023-03-19 03:16:25,439] [INFO] Selected 7 target genomes.
[2023-03-19 03:16:25,439] [INFO] Target genome list was writen to OceanDNA-b30238/target_genomes_gtdb.txt
[2023-03-19 03:16:25,464] [INFO] Task started: fastANI
[2023-03-19 03:16:25,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb0f25a-c231-4b21-803d-2c5ea87f0433/OceanDNA-b30238.fa --refList OceanDNA-b30238/target_genomes_gtdb.txt --output OceanDNA-b30238/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:16:31,357] [INFO] Task succeeded: fastANI
[2023-03-19 03:16:31,362] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:16:31,362] [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_900113435.1	s__Sulfitobacter dubius	97.7837	1039	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	conclusive
GCF_003611275.1	s__Sulfitobacter sp001634775	89.8292	945	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCA_002703405.1	s__Sulfitobacter sp002703405	89.3771	801	1119	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	88.0137	890	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_000172095.1	s__Sulfitobacter indolifex	87.3911	909	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102535.1	s__Sulfitobacter delicatus	84.4317	811	1119	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	83.9684	761	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:16:31,363] [INFO] GTDB search result was written to OceanDNA-b30238/result_gtdb.tsv
[2023-03-19 03:16:31,363] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:16:31,365] [INFO] DFAST_QC result json was written to OceanDNA-b30238/dqc_result.json
[2023-03-19 03:16:31,365] [INFO] DFAST_QC completed!
[2023-03-19 03:16:31,365] [INFO] Total running time: 0h1m33s