[2023-03-17 10:08:39,429] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference
[2023-03-17 10:08:40,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,540] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,540] [INFO] Running command: cat /var/lib/cwl/stg8844e867-c5dc-4585-baf9-da2a865b01ce/OceanDNA-b24012.fa | prodigal -d OceanDNA-b24012/cds.fna -a OceanDNA-b24012/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:09:01,829] [INFO] Task succeeded: Prodigal
[2023-03-17 10:09:01,829] [INFO] Task started: HMMsearch
[2023-03-17 10:09:01,829] [INFO] Running command: hmmsearch --tblout OceanDNA-b24012/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference/reference_markers.hmm OceanDNA-b24012/protein.faa > /dev/null
[2023-03-17 10:09:02,041] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:09:02,041] [INFO] Found 6/6 markers.
[2023-03-17 10:09:02,118] [INFO] Query marker FASTA was written to OceanDNA-b24012/markers.fasta
[2023-03-17 10:09:02,120] [INFO] Task started: Blastn
[2023-03-17 10:09:02,120] [INFO] Running command: blastn -query OceanDNA-b24012/markers.fasta -db /var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference/reference_markers.fasta -out OceanDNA-b24012/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:02,961] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:02,972] [INFO] Selected 24 target genomes.
[2023-03-17 10:09:02,973] [INFO] Target genome list was writen to OceanDNA-b24012/target_genomes.txt
[2023-03-17 10:09:02,994] [INFO] Task started: fastANI
[2023-03-17 10:09:02,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg8844e867-c5dc-4585-baf9-da2a865b01ce/OceanDNA-b24012.fa --refList OceanDNA-b24012/target_genomes.txt --output OceanDNA-b24012/fastani_result.tsv --threads 1
[2023-03-17 10:09:20,624] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:20,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:09:20,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:09:20,647] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:09:20,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:09:20,647] [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	79.9417	622	1049	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.8472	136	1049	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	76.8017	123	1049	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.7913	145	1049	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.7809	145	1049	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	76.7551	255	1049	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	76.7513	253	1049	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	76.1945	93	1049	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.0354	60	1049	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	75.9981	60	1049	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	75.9312	72	1049	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	75.9184	76	1049	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	75.7861	91	1049	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	75.7563	64	1049	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.7187	81	1049	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	75.6592	70	1049	95	below_threshold
Bradyrhizobium shewense	strain=ERR11	GCA_900094605.1	1761772	1761772	type	True	75.6203	94	1049	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	75.5227	100	1049	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	75.5122	104	1049	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	75.4893	98	1049	95	below_threshold
Bradyrhizobium yuanmingense	strain=CCBAU 10071	GCA_900094575.1	108015	108015	type	True	75.4686	83	1049	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.2479	57	1049	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:09:20,652] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24012/tc_result.tsv
[2023-03-17 10:09:20,652] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:09:20,652] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:09:20,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference/checkm_data
[2023-03-17 10:09:20,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:09:20,689] [INFO] Task started: CheckM
[2023-03-17 10:09:20,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24012/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24012/checkm_input OceanDNA-b24012/checkm_result
[2023-03-17 10:10:11,539] [INFO] Task succeeded: CheckM
[2023-03-17 10:10:11,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.12%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:10:11,745] [INFO] ===== Completeness check finished =====
[2023-03-17 10:10:11,745] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:10:11,746] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24012/markers.fasta)
[2023-03-17 10:10:11,747] [INFO] Task started: Blastn
[2023-03-17 10:10:11,747] [INFO] Running command: blastn -query OceanDNA-b24012/markers.fasta -db /var/lib/cwl/stg8be578b9-7153-40cf-9d0a-5a43b986aecf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24012/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:10:13,617] [INFO] Task succeeded: Blastn
[2023-03-17 10:10:13,645] [INFO] Selected 14 target genomes.
[2023-03-17 10:10:13,645] [INFO] Target genome list was writen to OceanDNA-b24012/target_genomes_gtdb.txt
[2023-03-17 10:10:13,693] [INFO] Task started: fastANI
[2023-03-17 10:10:13,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg8844e867-c5dc-4585-baf9-da2a865b01ce/OceanDNA-b24012.fa --refList OceanDNA-b24012/target_genomes_gtdb.txt --output OceanDNA-b24012/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:10:22,698] [INFO] Task succeeded: fastANI
[2023-03-17 10:10:22,706] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:10:22,706] [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	79.9455	622	1049	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	79.4433	547	1049	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	78.227	367	1049	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	77.4748	317	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826095.1	s__CV81 sp902826095	76.9944	209	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002535.1	s__Marinicaulis sp013002535	76.8434	162	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	99.52	99.49	0.97	0.96	3	-
GCA_001767925.1	s__CV81 sp001767925	76.8387	220	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125425.1	s__Amphiplicatus sp016125425	76.7744	207	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151435.1	s__Marinicaulis sp013151435	76.1844	103	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	97.18	97.18	0.82	0.82	2	-
GCF_002088945.1	s__Henriciella pelagia	76.0354	60	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004570865.1	s__Bradyrhizobium frederickii	75.7861	91	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	97.35	97.32	0.89	0.89	3	-
GCF_001375595.1	s__Phenylobacterium immobile	75.7264	57	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811655.1	s__Methylosinus sp009811655	75.5408	83	1049	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:10:22,710] [INFO] GTDB search result was written to OceanDNA-b24012/result_gtdb.tsv
[2023-03-17 10:10:22,720] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:10:22,733] [INFO] DFAST_QC result json was written to OceanDNA-b24012/dqc_result.json
[2023-03-17 10:10:22,733] [INFO] DFAST_QC completed!
[2023-03-17 10:10:22,733] [INFO] Total running time: 0h1m43s