[2023-03-14 13:46:33,108] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:46:33,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:46:33,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference
[2023-03-14 13:46:34,234] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:46:34,234] [INFO] Task started: Prodigal
[2023-03-14 13:46:34,234] [INFO] Running command: cat /var/lib/cwl/stgf7fb9e3c-7657-4f49-8979-7f21d21dafac/OceanDNA-b29571.fa | prodigal -d OceanDNA-b29571/cds.fna -a OceanDNA-b29571/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:46:43,629] [INFO] Task succeeded: Prodigal
[2023-03-14 13:46:43,629] [INFO] Task started: HMMsearch
[2023-03-14 13:46:43,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b29571/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference/reference_markers.hmm OceanDNA-b29571/protein.faa > /dev/null
[2023-03-14 13:46:43,789] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:46:43,789] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf7fb9e3c-7657-4f49-8979-7f21d21dafac/OceanDNA-b29571.fa]
[2023-03-14 13:46:43,807] [INFO] Query marker FASTA was written to OceanDNA-b29571/markers.fasta
[2023-03-14 13:46:43,807] [INFO] Task started: Blastn
[2023-03-14 13:46:43,808] [INFO] Running command: blastn -query OceanDNA-b29571/markers.fasta -db /var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference/reference_markers.fasta -out OceanDNA-b29571/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:46:44,276] [INFO] Task succeeded: Blastn
[2023-03-14 13:46:44,276] [INFO] Selected 19 target genomes.
[2023-03-14 13:46:44,277] [INFO] Target genome list was writen to OceanDNA-b29571/target_genomes.txt
[2023-03-14 13:46:44,285] [INFO] Task started: fastANI
[2023-03-14 13:46:44,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7fb9e3c-7657-4f49-8979-7f21d21dafac/OceanDNA-b29571.fa --refList OceanDNA-b29571/target_genomes.txt --output OceanDNA-b29571/fastani_result.tsv --threads 1
[2023-03-14 13:46:54,660] [INFO] Task succeeded: fastANI
[2023-03-14 13:46:54,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:46:54,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:46:54,670] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:46:54,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:46:54,670] [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
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.5281	135	392	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.3808	119	392	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.9888	66	392	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.9215	73	392	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.7658	64	392	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.7326	64	392	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.7185	79	392	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.6577	57	392	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.6053	90	392	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.5948	54	392	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	76.536	65	392	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.5177	56	392	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	76.5118	63	392	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.4466	61	392	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.0909	65	392	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.0784	54	392	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:46:54,670] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29571/tc_result.tsv
[2023-03-14 13:46:54,670] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:46:54,670] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:46:54,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference/checkm_data
[2023-03-14 13:46:54,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:46:54,675] [INFO] Task started: CheckM
[2023-03-14 13:46:54,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29571/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29571/checkm_input OceanDNA-b29571/checkm_result
[2023-03-14 13:47:22,713] [INFO] Task succeeded: CheckM
[2023-03-14 13:47:22,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 32.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:47:22,715] [INFO] ===== Completeness check finished =====
[2023-03-14 13:47:22,715] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:47:22,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29571/markers.fasta)
[2023-03-14 13:47:22,716] [INFO] Task started: Blastn
[2023-03-14 13:47:22,716] [INFO] Running command: blastn -query OceanDNA-b29571/markers.fasta -db /var/lib/cwl/stg3d33d782-29ea-474b-84aa-07460ee6fa96/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29571/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:47:23,204] [INFO] Task succeeded: Blastn
[2023-03-14 13:47:23,205] [INFO] Selected 20 target genomes.
[2023-03-14 13:47:23,205] [INFO] Target genome list was writen to OceanDNA-b29571/target_genomes_gtdb.txt
[2023-03-14 13:47:23,218] [INFO] Task started: fastANI
[2023-03-14 13:47:23,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7fb9e3c-7657-4f49-8979-7f21d21dafac/OceanDNA-b29571.fa --refList OceanDNA-b29571/target_genomes_gtdb.txt --output OceanDNA-b29571/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:47:35,169] [INFO] Task succeeded: fastANI
[2023-03-14 13:47:35,178] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:47:35,179] [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
GCA_009697225.1	s__Halovulum marinum	77.5281	135	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	76.9515	67	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCA_019061145.1	s__ASV31 sp019061145	76.8987	71	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.8643	73	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	76.7658	64	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.7231	58	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.7185	79	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	76.6577	57	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_900142935.1	s__Rhodovulum sp900142935	76.6511	74	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003500165.1	s__UBA10424 sp003500165	76.6388	67	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA10424	95.0	99.72	99.62	0.98	0.98	3	-
GCF_009363655.1	s__Roseovarius sp009363655	76.5785	57	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.5529	77	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094885.1	s__Salibaculum halophilum	76.5118	63	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359745.1	s__JACIYW01 sp014359745	76.3419	53	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	76.2575	72	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	76.0909	65	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	75.8397	61	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:47:35,179] [INFO] GTDB search result was written to OceanDNA-b29571/result_gtdb.tsv
[2023-03-14 13:47:35,179] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:47:35,181] [INFO] DFAST_QC result json was written to OceanDNA-b29571/dqc_result.json
[2023-03-14 13:47:35,181] [INFO] DFAST_QC completed!
[2023-03-14 13:47:35,181] [INFO] Total running time: 0h1m2s