[2023-03-15 10:34:47,901] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:34:47,917] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:34:47,917] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference
[2023-03-15 10:34:49,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:34:49,423] [INFO] Task started: Prodigal
[2023-03-15 10:34:49,423] [INFO] Running command: cat /var/lib/cwl/stg43f09333-d2bf-43b4-b9ad-599f33737974/OceanDNA-b24946.fa | prodigal -d OceanDNA-b24946/cds.fna -a OceanDNA-b24946/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:35:07,800] [INFO] Task succeeded: Prodigal
[2023-03-15 10:35:07,800] [INFO] Task started: HMMsearch
[2023-03-15 10:35:07,800] [INFO] Running command: hmmsearch --tblout OceanDNA-b24946/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference/reference_markers.hmm OceanDNA-b24946/protein.faa > /dev/null
[2023-03-15 10:35:08,009] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:35:08,009] [INFO] Found 6/6 markers.
[2023-03-15 10:35:08,135] [INFO] Query marker FASTA was written to OceanDNA-b24946/markers.fasta
[2023-03-15 10:35:08,136] [INFO] Task started: Blastn
[2023-03-15 10:35:08,137] [INFO] Running command: blastn -query OceanDNA-b24946/markers.fasta -db /var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference/reference_markers.fasta -out OceanDNA-b24946/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:35:09,050] [INFO] Task succeeded: Blastn
[2023-03-15 10:35:09,099] [INFO] Selected 22 target genomes.
[2023-03-15 10:35:09,100] [INFO] Target genome list was writen to OceanDNA-b24946/target_genomes.txt
[2023-03-15 10:35:09,111] [INFO] Task started: fastANI
[2023-03-15 10:35:09,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f09333-d2bf-43b4-b9ad-599f33737974/OceanDNA-b24946.fa --refList OceanDNA-b24946/target_genomes.txt --output OceanDNA-b24946/fastani_result.tsv --threads 1
[2023-03-15 10:35:28,233] [INFO] Task succeeded: fastANI
[2023-03-15 10:35:28,234] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:35:28,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:35:28,247] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:35:28,247] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:35:28,247] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	82.1891	719	997	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.7838	505	997	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.4217	484	997	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.5627	271	997	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.1612	199	997	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	76.9611	132	997	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.8292	191	997	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	76.772	142	997	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	76.7689	154	997	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.7281	192	997	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.7121	143	997	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.6814	119	997	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	76.6499	162	997	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	76.6259	162	997	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.5837	173	997	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.577	134	997	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.4732	156	997	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.4521	173	997	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.4259	143	997	95	below_threshold
Chelatococcus asaccharovorans	strain=DSM 6462	GCA_003201475.1	28210	28210	type	True	76.3704	133	997	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.3589	139	997	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.2865	143	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:35:28,264] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24946/tc_result.tsv
[2023-03-15 10:35:28,290] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:35:28,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:35:28,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference/checkm_data
[2023-03-15 10:35:28,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:35:28,307] [INFO] Task started: CheckM
[2023-03-15 10:35:28,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24946/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24946/checkm_input OceanDNA-b24946/checkm_result
[2023-03-15 10:36:15,447] [INFO] Task succeeded: CheckM
[2023-03-15 10:36:15,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:36:15,779] [INFO] ===== Completeness check finished =====
[2023-03-15 10:36:15,780] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:36:15,780] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24946/markers.fasta)
[2023-03-15 10:36:15,781] [INFO] Task started: Blastn
[2023-03-15 10:36:15,781] [INFO] Running command: blastn -query OceanDNA-b24946/markers.fasta -db /var/lib/cwl/stg6c08e7c4-95da-4be8-a116-b80702e29d60/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24946/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:36:17,580] [INFO] Task succeeded: Blastn
[2023-03-15 10:36:17,623] [INFO] Selected 10 target genomes.
[2023-03-15 10:36:17,623] [INFO] Target genome list was writen to OceanDNA-b24946/target_genomes_gtdb.txt
[2023-03-15 10:36:18,007] [INFO] Task started: fastANI
[2023-03-15 10:36:18,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f09333-d2bf-43b4-b9ad-599f33737974/OceanDNA-b24946.fa --refList OceanDNA-b24946/target_genomes_gtdb.txt --output OceanDNA-b24946/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:36:27,090] [INFO] Task succeeded: fastANI
[2023-03-15 10:36:27,097] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:36:27,097] [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_014359855.1	s__Parvibaculum sp014359855	91.13	531	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	90.0948	789	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	84.7726	795	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_002694985.1	s__Parvibaculum sp002694985	83.3929	747	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017642695.1	s__Parvibaculum sp017642695	83.0082	763	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	82.2028	718	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531575.1	s__Bradyrhizobium sp002531575	76.6231	180	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219575.1	s__Bradyrhizobium sp016219575	76.4919	162	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129425.1	s__Bradyrhizobium erythrophlei_C	76.3396	126	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.1234	114	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:36:27,110] [INFO] GTDB search result was written to OceanDNA-b24946/result_gtdb.tsv
[2023-03-15 10:36:27,138] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:36:27,156] [INFO] DFAST_QC result json was written to OceanDNA-b24946/dqc_result.json
[2023-03-15 10:36:27,156] [INFO] DFAST_QC completed!
[2023-03-15 10:36:27,156] [INFO] Total running time: 0h1m39s