[2023-03-19 01:50:01,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference
[2023-03-19 01:50:03,570] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,571] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,571] [INFO] Running command: cat /var/lib/cwl/stg48eddd42-afa7-4818-be57-8adf6f18769a/OceanDNA-b30397.fa | prodigal -d OceanDNA-b30397/cds.fna -a OceanDNA-b30397/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:24,155] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:24,155] [INFO] Task started: HMMsearch
[2023-03-19 01:50:24,155] [INFO] Running command: hmmsearch --tblout OceanDNA-b30397/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference/reference_markers.hmm OceanDNA-b30397/protein.faa > /dev/null
[2023-03-19 01:50:24,350] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:24,350] [INFO] Found 6/6 markers.
[2023-03-19 01:50:24,371] [INFO] Query marker FASTA was written to OceanDNA-b30397/markers.fasta
[2023-03-19 01:50:24,371] [INFO] Task started: Blastn
[2023-03-19 01:50:24,371] [INFO] Running command: blastn -query OceanDNA-b30397/markers.fasta -db /var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference/reference_markers.fasta -out OceanDNA-b30397/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:25,092] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:25,093] [INFO] Selected 10 target genomes.
[2023-03-19 01:50:25,093] [INFO] Target genome list was writen to OceanDNA-b30397/target_genomes.txt
[2023-03-19 01:50:25,099] [INFO] Task started: fastANI
[2023-03-19 01:50:25,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg48eddd42-afa7-4818-be57-8adf6f18769a/OceanDNA-b30397.fa --refList OceanDNA-b30397/target_genomes.txt --output OceanDNA-b30397/fastani_result.tsv --threads 1
[2023-03-19 01:50:32,676] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:32,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:32,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:32,684] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:32,684] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:32,684] [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	90.1306	938	1057	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	87.3192	937	1057	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	87.2986	943	1057	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	84.6327	839	1057	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	84.281	784	1057	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.6491	364	1057	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.2277	232	1057	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.0376	224	1057	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7456	256	1057	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.6439	207	1057	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:32,684] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30397/tc_result.tsv
[2023-03-19 01:50:32,684] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:32,684] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:32,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference/checkm_data
[2023-03-19 01:50:32,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:32,689] [INFO] Task started: CheckM
[2023-03-19 01:50:32,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30397/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30397/checkm_input OceanDNA-b30397/checkm_result
[2023-03-19 01:51:24,892] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:24,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:24,897] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:24,897] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:24,898] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30397/markers.fasta)
[2023-03-19 01:51:24,899] [INFO] Task started: Blastn
[2023-03-19 01:51:24,899] [INFO] Running command: blastn -query OceanDNA-b30397/markers.fasta -db /var/lib/cwl/stgbad6add8-4df6-47b8-ab6b-cba7c7f722b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30397/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:26,115] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:26,125] [INFO] Selected 7 target genomes.
[2023-03-19 01:51:26,125] [INFO] Target genome list was writen to OceanDNA-b30397/target_genomes_gtdb.txt
[2023-03-19 01:51:26,129] [INFO] Task started: fastANI
[2023-03-19 01:51:26,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg48eddd42-afa7-4818-be57-8adf6f18769a/OceanDNA-b30397.fa --refList OceanDNA-b30397/target_genomes_gtdb.txt --output OceanDNA-b30397/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:32,145] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:32,150] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-19 01:51:32,150] [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_003611275.1	s__Sulfitobacter sp001634775	96.6111	1026	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	inconclusive
GCA_002703405.1	s__Sulfitobacter sp002703405	96.6092	882	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	inconclusive
GCF_900113435.1	s__Sulfitobacter dubius	90.1306	938	1057	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_017743885.1	s__Sulfitobacter sp001635605	89.513	956	1057	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	87.3284	936	1057	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	84.6327	839	1057	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	84.2716	785	1057	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 01:51:32,151] [INFO] GTDB search result was written to OceanDNA-b30397/result_gtdb.tsv
[2023-03-19 01:51:32,151] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:32,152] [INFO] DFAST_QC result json was written to OceanDNA-b30397/dqc_result.json
[2023-03-19 01:51:32,152] [INFO] DFAST_QC completed!
[2023-03-19 01:51:32,152] [INFO] Total running time: 0h1m30s