[2023-03-14 12:03:55,347] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,352] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference
[2023-03-14 12:03:56,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,864] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,864] [INFO] Running command: cat /var/lib/cwl/stg5499986a-63c3-4edf-be5d-b7bcb05e2e61/OceanDNA-b26660.fa | prodigal -d OceanDNA-b26660/cds.fna -a OceanDNA-b26660/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:22,647] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:22,647] [INFO] Task started: HMMsearch
[2023-03-14 12:04:22,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b26660/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference/reference_markers.hmm OceanDNA-b26660/protein.faa > /dev/null
[2023-03-14 12:04:22,888] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:22,889] [INFO] Found 6/6 markers.
[2023-03-14 12:04:22,925] [INFO] Query marker FASTA was written to OceanDNA-b26660/markers.fasta
[2023-03-14 12:04:22,926] [INFO] Task started: Blastn
[2023-03-14 12:04:22,926] [INFO] Running command: blastn -query OceanDNA-b26660/markers.fasta -db /var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference/reference_markers.fasta -out OceanDNA-b26660/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:23,990] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:23,996] [INFO] Selected 26 target genomes.
[2023-03-14 12:04:23,997] [INFO] Target genome list was writen to OceanDNA-b26660/target_genomes.txt
[2023-03-14 12:04:24,025] [INFO] Task started: fastANI
[2023-03-14 12:04:24,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg5499986a-63c3-4edf-be5d-b7bcb05e2e61/OceanDNA-b26660.fa --refList OceanDNA-b26660/target_genomes.txt --output OceanDNA-b26660/fastani_result.tsv --threads 1
[2023-03-14 12:04:47,423] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:47,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:47,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:47,438] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:47,438] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:04:47,438] [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
Amorphus coralli	strain=DSM 19760	GCA_000374525.1	340680	340680	type	True	85.6644	1006	1429	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.8641	394	1429	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.7986	396	1429	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	77.6396	419	1429	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.5958	353	1429	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	77.4947	390	1429	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	77.3675	333	1429	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	77.3171	266	1429	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	77.3103	413	1429	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	77.2941	359	1429	95	below_threshold
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	77.2898	450	1429	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	77.2701	366	1429	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.2601	299	1429	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.2499	464	1429	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.217	374	1429	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	77.0998	336	1429	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	77.0779	337	1429	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	77.0624	330	1429	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	76.7854	279	1429	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	76.7531	401	1429	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.7051	349	1429	95	below_threshold
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	76.5305	251	1429	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.5025	289	1429	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.5011	394	1429	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.4709	299	1429	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.3091	282	1429	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:47,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26660/tc_result.tsv
[2023-03-14 12:04:47,442] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:47,442] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:47,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference/checkm_data
[2023-03-14 12:04:47,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:47,483] [INFO] Task started: CheckM
[2023-03-14 12:04:47,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26660/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26660/checkm_input OceanDNA-b26660/checkm_result
[2023-03-14 12:05:50,250] [INFO] Task succeeded: CheckM
[2023-03-14 12:05:50,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:05:50,309] [INFO] ===== Completeness check finished =====
[2023-03-14 12:05:50,309] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:05:50,310] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26660/markers.fasta)
[2023-03-14 12:05:50,311] [INFO] Task started: Blastn
[2023-03-14 12:05:50,311] [INFO] Running command: blastn -query OceanDNA-b26660/markers.fasta -db /var/lib/cwl/stg50d4a655-e96a-4044-babf-3e4e1bd5163b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26660/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:05:52,530] [INFO] Task succeeded: Blastn
[2023-03-14 12:05:52,550] [INFO] Selected 24 target genomes.
[2023-03-14 12:05:52,550] [INFO] Target genome list was writen to OceanDNA-b26660/target_genomes_gtdb.txt
[2023-03-14 12:05:52,575] [INFO] Task started: fastANI
[2023-03-14 12:05:52,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg5499986a-63c3-4edf-be5d-b7bcb05e2e61/OceanDNA-b26660.fa --refList OceanDNA-b26660/target_genomes_gtdb.txt --output OceanDNA-b26660/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:06:13,161] [INFO] Task succeeded: fastANI
[2023-03-14 12:06:13,174] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:06:13,174] [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_000374525.1	s__Amorphus coralli	85.6378	1009	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610575.1	s__Stappia sp003610575	77.7519	376	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCF_900185725.1	s__Stappia sp900185725	77.6802	407	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_016411865.1	s__Acuticoccus sp016411865	77.6548	417	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789575.1	s__Stappia indica_A	77.6074	406	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	77.5739	356	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148505.1	s__Pseudoxanthobacter soli	77.5076	332	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	77.4615	402	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	77.4045	328	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869065.1	s__Rhodobium sp002869065	77.3829	292	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258595.1	s__Acuticoccus sediminis	77.2837	450	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839445.1	s__Chthonobacter albigriseus	77.2737	300	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	77.2437	465	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCA_002722295.1	s__Stappia sp002722295	77.1419	281	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
GCF_003667445.1	s__Xanthobacter tagetidis	77.1076	334	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017872635.1	s__Starkeya sp017872635	77.0239	349	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	76.9464	330	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	76.9196	262	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	76.8566	365	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	76.7943	290	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	76.7767	281	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390695.1	s__Ancylobacter_B sonchi	76.7082	409	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187085.1	s__Pseudorhodoplanes sp019187085	76.6733	241	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudorhodoplanes	95.0	98.90	98.90	0.85	0.85	2	-
GCF_006151805.1	s__Methylobacterium sp006151805	76.4835	397	1429	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:06:13,177] [INFO] GTDB search result was written to OceanDNA-b26660/result_gtdb.tsv
[2023-03-14 12:06:13,183] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:06:13,188] [INFO] DFAST_QC result json was written to OceanDNA-b26660/dqc_result.json
[2023-03-14 12:06:13,188] [INFO] DFAST_QC completed!
[2023-03-14 12:06:13,188] [INFO] Total running time: 0h2m18s