[2023-03-18 09:53:10,264] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,264] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,264] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference
[2023-03-18 09:53:11,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,411] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,411] [INFO] Running command: cat /var/lib/cwl/stga4b0d1ed-f05f-4be0-aab4-32aa9b139006/OceanDNA-b33304.fa | prodigal -d OceanDNA-b33304/cds.fna -a OceanDNA-b33304/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:29,905] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:29,905] [INFO] Task started: HMMsearch
[2023-03-18 09:53:29,905] [INFO] Running command: hmmsearch --tblout OceanDNA-b33304/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference/reference_markers.hmm OceanDNA-b33304/protein.faa > /dev/null
[2023-03-18 09:53:30,104] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:30,105] [INFO] Found 6/6 markers.
[2023-03-18 09:53:30,122] [INFO] Query marker FASTA was written to OceanDNA-b33304/markers.fasta
[2023-03-18 09:53:30,123] [INFO] Task started: Blastn
[2023-03-18 09:53:30,123] [INFO] Running command: blastn -query OceanDNA-b33304/markers.fasta -db /var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference/reference_markers.fasta -out OceanDNA-b33304/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:30,769] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:30,770] [INFO] Selected 27 target genomes.
[2023-03-18 09:53:30,770] [INFO] Target genome list was writen to OceanDNA-b33304/target_genomes.txt
[2023-03-18 09:53:30,807] [INFO] Task started: fastANI
[2023-03-18 09:53:30,807] [INFO] Running command: fastANI --query /var/lib/cwl/stga4b0d1ed-f05f-4be0-aab4-32aa9b139006/OceanDNA-b33304.fa --refList OceanDNA-b33304/target_genomes.txt --output OceanDNA-b33304/fastani_result.tsv --threads 1
[2023-03-18 09:53:50,993] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:50,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:53:50,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:53:51,008] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:53:51,008] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:53:51,008] [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
Herminiimonas arsenitoxidans	strain=AS8	GCA_900130075.1	1809410	1809410	type	True	78.963	299	956	95	below_threshold
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	78.6426	337	956	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	78.636	341	956	95	below_threshold
Oxalicibacterium faecigallinarum	strain=CCM 2767	GCA_014635705.1	573741	573741	type	True	77.7805	224	956	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	77.4236	145	956	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	77.3593	136	956	95	below_threshold
Glaciimonas immobilis	strain=DSM 23240	GCA_014202815.1	728004	728004	type	True	77.2902	111	956	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	77.2736	137	956	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	77.2216	117	956	95	below_threshold
Collimonas antrihumi	strain=DSM 104040	GCA_018304965.1	1940615	1940615	type	True	77.1939	142	956	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	77.1327	134	956	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	77.0776	136	956	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	77.0563	143	956	95	below_threshold
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	77.0407	102	956	95	below_threshold
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	77.0205	99	956	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	76.9388	81	956	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.7568	120	956	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	76.667	76	956	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.6571	91	956	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	76.6499	100	956	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	76.6235	94	956	95	below_threshold
Undibacterium parvum	strain=DSM 23061	GCA_003955735.1	401471	401471	type	True	76.5795	92	956	95	below_threshold
Janthinobacterium agaricidamnosum	strain=NBRC 102515	GCA_001571185.1	55508	55508	type	True	76.5699	114	956	95	below_threshold
Undibacterium squillarum	strain=KCTC 23917	GCA_014652435.1	1131567	1131567	type	True	76.5664	78	956	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.3979	91	956	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	76.3224	84	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:53:51,008] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33304/tc_result.tsv
[2023-03-18 09:53:51,008] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:53:51,009] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:51,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference/checkm_data
[2023-03-18 09:53:51,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:51,083] [INFO] Task started: CheckM
[2023-03-18 09:53:51,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33304/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33304/checkm_input OceanDNA-b33304/checkm_result
[2023-03-18 09:54:38,682] [INFO] Task succeeded: CheckM
[2023-03-18 09:54:38,682] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:54:38,684] [INFO] ===== Completeness check finished =====
[2023-03-18 09:54:38,684] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:54:38,684] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33304/markers.fasta)
[2023-03-18 09:54:38,686] [INFO] Task started: Blastn
[2023-03-18 09:54:38,686] [INFO] Running command: blastn -query OceanDNA-b33304/markers.fasta -db /var/lib/cwl/stgdc0514e1-ad96-45a1-afaf-d3c101c44245/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33304/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:54:39,776] [INFO] Task succeeded: Blastn
[2023-03-18 09:54:39,777] [INFO] Selected 22 target genomes.
[2023-03-18 09:54:39,777] [INFO] Target genome list was writen to OceanDNA-b33304/target_genomes_gtdb.txt
[2023-03-18 09:54:39,851] [INFO] Task started: fastANI
[2023-03-18 09:54:39,851] [INFO] Running command: fastANI --query /var/lib/cwl/stga4b0d1ed-f05f-4be0-aab4-32aa9b139006/OceanDNA-b33304.fa --refList OceanDNA-b33304/target_genomes_gtdb.txt --output OceanDNA-b33304/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:54:54,357] [INFO] Task succeeded: fastANI
[2023-03-18 09:54:54,369] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:54:54,370] [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_900130075.1	s__Herminiimonas arsenitoxidans	78.963	299	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464355.1	s__Herminiimonas sp001464355	78.8194	333	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000026125.1	s__Herminiimonas arsenicoxydans	78.7796	320	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645465.1	s__Herminiimonas contaminans	78.7739	287	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	97.73	97.73	0.94	0.94	3	-
GCF_003293745.1	s__Herminiimonas fonticola	78.6426	337	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000013625.1	s__Herminiimonas sp000013625	78.6239	281	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852535.1	s__Herminiimonas sp003852535	78.5399	262	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384815.1	s__Herminiimonas sp002384815	78.3074	271	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635705.1	s__Oxalicibacterium faecigallinarum	77.7952	223	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018305005.1	s__Collimonas sp018305005	77.4236	145	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	77.3724	132	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCA_004134995.1	s__Herbaspirillum sp004134995	77.3659	120	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111995.1	s__Collimonas sp900111995	77.2599	141	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112135.1	s__Collimonas sp900112135	77.2572	133	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_001584145.1	s__Collimonas fungivorans	77.1327	134	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189915.1	s__Herbaspirillum autotrophicum	77.0613	145	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927625.1	s__AVCC01 sp012927625	76.9441	90	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770855.1	s__MESE01 sp001770855	76.9326	126	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MESE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590875.1	s__Noviherbaspirillum sp003590875	76.7568	120	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241865.1	s__Paucimonas sp018241865	76.723	102	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927585.1	s__AVCC01 sp012927585	76.6979	99	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862415.1	s__Solimicrobium sp903862415	76.4212	79	956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Solimicrobium	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:54:54,370] [INFO] GTDB search result was written to OceanDNA-b33304/result_gtdb.tsv
[2023-03-18 09:54:54,370] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:54:54,372] [INFO] DFAST_QC result json was written to OceanDNA-b33304/dqc_result.json
[2023-03-18 09:54:54,372] [INFO] DFAST_QC completed!
[2023-03-18 09:54:54,373] [INFO] Total running time: 0h1m44s