[2023-03-16 00:05:33,360] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:05:33,360] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:05:33,360] [INFO] DQC Reference Directory: /var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference
[2023-03-16 00:05:34,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:05:34,458] [INFO] Task started: Prodigal
[2023-03-16 00:05:34,458] [INFO] Running command: cat /var/lib/cwl/stgce373c11-628e-44e4-a5df-25b197e9211b/OceanDNA-b30459.fa | prodigal -d OceanDNA-b30459/cds.fna -a OceanDNA-b30459/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:05:50,928] [INFO] Task succeeded: Prodigal
[2023-03-16 00:05:50,928] [INFO] Task started: HMMsearch
[2023-03-16 00:05:50,929] [INFO] Running command: hmmsearch --tblout OceanDNA-b30459/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference/reference_markers.hmm OceanDNA-b30459/protein.faa > /dev/null
[2023-03-16 00:05:51,116] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:05:51,117] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgce373c11-628e-44e4-a5df-25b197e9211b/OceanDNA-b30459.fa]
[2023-03-16 00:05:51,173] [INFO] Query marker FASTA was written to OceanDNA-b30459/markers.fasta
[2023-03-16 00:05:51,174] [INFO] Task started: Blastn
[2023-03-16 00:05:51,174] [INFO] Running command: blastn -query OceanDNA-b30459/markers.fasta -db /var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference/reference_markers.fasta -out OceanDNA-b30459/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:05:51,844] [INFO] Task succeeded: Blastn
[2023-03-16 00:05:51,859] [INFO] Selected 19 target genomes.
[2023-03-16 00:05:51,860] [INFO] Target genome list was writen to OceanDNA-b30459/target_genomes.txt
[2023-03-16 00:05:51,874] [INFO] Task started: fastANI
[2023-03-16 00:05:51,874] [INFO] Running command: fastANI --query /var/lib/cwl/stgce373c11-628e-44e4-a5df-25b197e9211b/OceanDNA-b30459.fa --refList OceanDNA-b30459/target_genomes.txt --output OceanDNA-b30459/fastani_result.tsv --threads 1
[2023-03-16 00:06:05,441] [INFO] Task succeeded: fastANI
[2023-03-16 00:06:05,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:06:05,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:06:05,453] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:06:05,453] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:06:05,453] [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
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	84.3748	647	828	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	84.3729	647	828	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.9394	381	828	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.1694	314	828	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.153	318	828	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.952	343	828	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.8938	275	828	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.7723	244	828	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.7441	323	828	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7041	266	828	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.7008	265	828	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.5811	231	828	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.411	247	828	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.1754	244	828	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.1606	219	828	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.1237	206	828	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.0153	217	828	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.8929	159	828	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8143	194	828	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:06:05,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30459/tc_result.tsv
[2023-03-16 00:06:05,453] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:06:05,453] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:06:05,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference/checkm_data
[2023-03-16 00:06:05,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:06:05,514] [INFO] Task started: CheckM
[2023-03-16 00:06:05,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30459/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30459/checkm_input OceanDNA-b30459/checkm_result
[2023-03-16 00:06:49,191] [INFO] Task succeeded: CheckM
[2023-03-16 00:06:49,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.48%
Contamintation: 2.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:06:49,207] [INFO] ===== Completeness check finished =====
[2023-03-16 00:06:49,207] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:06:49,207] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30459/markers.fasta)
[2023-03-16 00:06:49,208] [INFO] Task started: Blastn
[2023-03-16 00:06:49,208] [INFO] Running command: blastn -query OceanDNA-b30459/markers.fasta -db /var/lib/cwl/stgcefcff8f-2e30-4d3b-830b-113991a5ac64/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30459/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:06:50,262] [INFO] Task succeeded: Blastn
[2023-03-16 00:06:50,266] [INFO] Selected 9 target genomes.
[2023-03-16 00:06:50,266] [INFO] Target genome list was writen to OceanDNA-b30459/target_genomes_gtdb.txt
[2023-03-16 00:06:50,380] [INFO] Task started: fastANI
[2023-03-16 00:06:50,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgce373c11-628e-44e4-a5df-25b197e9211b/OceanDNA-b30459.fa --refList OceanDNA-b30459/target_genomes_gtdb.txt --output OceanDNA-b30459/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:06:57,588] [INFO] Task succeeded: fastANI
[2023-03-16 00:06:57,594] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:06:57,595] [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_000620505.1	s__Ascidiaceihabitans sp000620505	84.5923	653	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	84.3748	647	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	84.2428	620	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	83.8084	629	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.9503	380	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.5707	370	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018200035.1	s__Sulfitobacter sp018200035	78.4045	345	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	78.3446	326	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_001634885.1	s__Sulfitobacter sp001634885	77.8269	293	828	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
--------------------------------------------------------------------------------
[2023-03-16 00:06:57,599] [INFO] GTDB search result was written to OceanDNA-b30459/result_gtdb.tsv
[2023-03-16 00:06:57,602] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:06:57,606] [INFO] DFAST_QC result json was written to OceanDNA-b30459/dqc_result.json
[2023-03-16 00:06:57,606] [INFO] DFAST_QC completed!
[2023-03-16 00:06:57,606] [INFO] Total running time: 0h1m24s