[2023-03-15 05:29:10,768] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,768] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,768] [INFO] DQC Reference Directory: /var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference
[2023-03-15 05:29:12,384] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,384] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,384] [INFO] Running command: cat /var/lib/cwl/stg73ac3e94-4f8d-4dba-9510-f2a9f99cb6b0/OceanDNA-b24013.fa | prodigal -d OceanDNA-b24013/cds.fna -a OceanDNA-b24013/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:31,028] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:31,029] [INFO] Task started: HMMsearch
[2023-03-15 05:29:31,029] [INFO] Running command: hmmsearch --tblout OceanDNA-b24013/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference/reference_markers.hmm OceanDNA-b24013/protein.faa > /dev/null
[2023-03-15 05:29:31,257] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:31,258] [INFO] Found 6/6 markers.
[2023-03-15 05:29:31,282] [INFO] Query marker FASTA was written to OceanDNA-b24013/markers.fasta
[2023-03-15 05:29:31,282] [INFO] Task started: Blastn
[2023-03-15 05:29:31,282] [INFO] Running command: blastn -query OceanDNA-b24013/markers.fasta -db /var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference/reference_markers.fasta -out OceanDNA-b24013/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:32,065] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:32,066] [INFO] Selected 24 target genomes.
[2023-03-15 05:29:32,066] [INFO] Target genome list was writen to OceanDNA-b24013/target_genomes.txt
[2023-03-15 05:29:32,077] [INFO] Task started: fastANI
[2023-03-15 05:29:32,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ac3e94-4f8d-4dba-9510-f2a9f99cb6b0/OceanDNA-b24013.fa --refList OceanDNA-b24013/target_genomes.txt --output OceanDNA-b24013/fastani_result.tsv --threads 1
[2023-03-15 05:29:48,700] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:48,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:48,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:48,710] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:48,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:48,711] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	79.1419	443	1000	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.9063	98	1000	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.9021	95	1000	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	76.7673	167	1000	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	76.7403	173	1000	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	76.2587	51	1000	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.0578	58	1000	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	75.9569	51	1000	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	75.9277	52	1000	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.8808	74	1000	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	75.8765	51	1000	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	75.8	57	1000	95	below_threshold
Alsobacter metallidurans	strain=CGMCC 1.12214	GCA_014636935.1	340221	340221	type	True	75.7751	52	1000	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	75.756	75	1000	95	below_threshold
Bradyrhizobium daqingense	strain=CCBAU 15774	GCA_021044685.1	993502	993502	type	True	75.6562	55	1000	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	75.4172	56	1000	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:48,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24013/tc_result.tsv
[2023-03-15 05:29:48,711] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:48,711] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:48,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference/checkm_data
[2023-03-15 05:29:48,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:48,722] [INFO] Task started: CheckM
[2023-03-15 05:29:48,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24013/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24013/checkm_input OceanDNA-b24013/checkm_result
[2023-03-15 05:30:36,815] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:36,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:36,818] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:36,818] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:36,819] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24013/markers.fasta)
[2023-03-15 05:30:36,820] [INFO] Task started: Blastn
[2023-03-15 05:30:36,820] [INFO] Running command: blastn -query OceanDNA-b24013/markers.fasta -db /var/lib/cwl/stg9add0473-e760-4bbb-bcbb-3b23f5d30ec8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24013/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:38,281] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:38,282] [INFO] Selected 20 target genomes.
[2023-03-15 05:30:38,282] [INFO] Target genome list was writen to OceanDNA-b24013/target_genomes_gtdb.txt
[2023-03-15 05:30:38,304] [INFO] Task started: fastANI
[2023-03-15 05:30:38,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ac3e94-4f8d-4dba-9510-f2a9f99cb6b0/OceanDNA-b24013.fa --refList OceanDNA-b24013/target_genomes_gtdb.txt --output OceanDNA-b24013/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:52,131] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:52,140] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:30:52,140] [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_002943565.1	s__Marinicaulis flavus	79.1424	443	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	79.0779	443	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002388885.1	s__Marinicaulis sp002388885	78.1226	295	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657385.1	s__Marinicaulis sp001657385	77.2142	227	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	77.0823	136	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	76.886	71	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	76.8451	164	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	76.7604	159	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	76.7534	168	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.6919	133	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_013151255.1	s__Marinicaulis sp013151255	76.5063	189	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151435.1	s__Marinicaulis sp013151435	76.2874	97	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	97.18	97.18	0.82	0.82	2	-
GCF_012848855.1	s__Pyruvatibacter mobilis	75.9569	51	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000516555.1	s__P52-10 sp000516555	75.9502	54	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__P52-10	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009792355.1	s__Terricaulis silvestris	75.9344	54	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645695.1	s__Salinarimonas ramus	75.5176	52	1000	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:52,141] [INFO] GTDB search result was written to OceanDNA-b24013/result_gtdb.tsv
[2023-03-15 05:30:52,141] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:52,142] [INFO] DFAST_QC result json was written to OceanDNA-b24013/dqc_result.json
[2023-03-15 05:30:52,143] [INFO] DFAST_QC completed!
[2023-03-15 05:30:52,143] [INFO] Total running time: 0h1m41s