[2023-03-14 11:40:05,680] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,681] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,681] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference
[2023-03-14 11:40:06,772] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,772] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,773] [INFO] Running command: cat /var/lib/cwl/stgc6b64e1a-d229-438b-92c3-613afa565ce7/OceanDNA-b27557.fa | prodigal -d OceanDNA-b27557/cds.fna -a OceanDNA-b27557/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:22,045] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:22,045] [INFO] Task started: HMMsearch
[2023-03-14 11:40:22,045] [INFO] Running command: hmmsearch --tblout OceanDNA-b27557/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference/reference_markers.hmm OceanDNA-b27557/protein.faa > /dev/null
[2023-03-14 11:40:22,215] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:22,216] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc6b64e1a-d229-438b-92c3-613afa565ce7/OceanDNA-b27557.fa]
[2023-03-14 11:40:22,254] [INFO] Query marker FASTA was written to OceanDNA-b27557/markers.fasta
[2023-03-14 11:40:22,254] [INFO] Task started: Blastn
[2023-03-14 11:40:22,254] [INFO] Running command: blastn -query OceanDNA-b27557/markers.fasta -db /var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference/reference_markers.fasta -out OceanDNA-b27557/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:22,743] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:22,747] [INFO] Selected 15 target genomes.
[2023-03-14 11:40:22,747] [INFO] Target genome list was writen to OceanDNA-b27557/target_genomes.txt
[2023-03-14 11:40:22,756] [INFO] Task started: fastANI
[2023-03-14 11:40:22,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b64e1a-d229-438b-92c3-613afa565ce7/OceanDNA-b27557.fa --refList OceanDNA-b27557/target_genomes.txt --output OceanDNA-b27557/fastani_result.tsv --threads 1
[2023-03-14 11:40:33,085] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:33,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:33,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:33,095] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:33,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:40:33,095] [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
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	79.1537	350	790	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	79.0492	353	790	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.9037	353	790	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	78.7232	323	790	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.6474	334	790	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.4885	281	790	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	78.192	301	790	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.0912	161	790	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.0253	141	790	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	76.9927	143	790	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.9555	182	790	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.7662	129	790	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4399	113	790	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.4399	113	790	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.0857	114	790	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:40:33,097] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27557/tc_result.tsv
[2023-03-14 11:40:33,098] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:33,098] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:33,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference/checkm_data
[2023-03-14 11:40:33,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:33,106] [INFO] Task started: CheckM
[2023-03-14 11:40:33,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27557/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27557/checkm_input OceanDNA-b27557/checkm_result
[2023-03-14 11:41:14,267] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:14,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:14,328] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:14,328] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:14,328] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27557/markers.fasta)
[2023-03-14 11:41:14,328] [INFO] Task started: Blastn
[2023-03-14 11:41:14,329] [INFO] Running command: blastn -query OceanDNA-b27557/markers.fasta -db /var/lib/cwl/stgbbf1d9af-05a8-47bd-9cb6-c72d76a8c3cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27557/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:14,874] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:14,879] [INFO] Selected 15 target genomes.
[2023-03-14 11:41:14,879] [INFO] Target genome list was writen to OceanDNA-b27557/target_genomes_gtdb.txt
[2023-03-14 11:41:14,894] [INFO] Task started: fastANI
[2023-03-14 11:41:14,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6b64e1a-d229-438b-92c3-613afa565ce7/OceanDNA-b27557.fa --refList OceanDNA-b27557/target_genomes_gtdb.txt --output OceanDNA-b27557/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:26,380] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:26,389] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:26,389] [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_000813745.1	s__Leisingera sp000813745	79.3195	345	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	79.1673	349	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	79.0379	358	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	79.0294	354	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000473145.1	s__Leisingera daeponensis	78.9036	353	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_013317235.1	s__Leisingera sp013317235	78.8811	342	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	78.8375	344	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	78.8304	322	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	78.7232	323	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	78.5437	310	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	78.4885	281	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373325.1	s__Leisingera sp013373325	78.4777	291	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302455.1	s__Ruegeria_E mediterranea	78.2047	300	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_900537075.1	s__Ruegeria_E sp900537075	77.612	231	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.168	151	790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:26,392] [INFO] GTDB search result was written to OceanDNA-b27557/result_gtdb.tsv
[2023-03-14 11:41:26,393] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:26,397] [INFO] DFAST_QC result json was written to OceanDNA-b27557/dqc_result.json
[2023-03-14 11:41:26,397] [INFO] DFAST_QC completed!
[2023-03-14 11:41:26,397] [INFO] Total running time: 0h1m21s