[2023-03-16 08:02:40,400] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:02:40,400] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:02:40,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference
[2023-03-16 08:02:41,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:02:41,599] [INFO] Task started: Prodigal
[2023-03-16 08:02:41,599] [INFO] Running command: cat /var/lib/cwl/stg76894d78-5a71-4c36-8f90-0401b7c5958b/OceanDNA-b27551.fa | prodigal -d OceanDNA-b27551/cds.fna -a OceanDNA-b27551/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:03:06,207] [INFO] Task succeeded: Prodigal
[2023-03-16 08:03:06,208] [INFO] Task started: HMMsearch
[2023-03-16 08:03:06,208] [INFO] Running command: hmmsearch --tblout OceanDNA-b27551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference/reference_markers.hmm OceanDNA-b27551/protein.faa > /dev/null
[2023-03-16 08:03:06,405] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:03:06,406] [INFO] Found 6/6 markers.
[2023-03-16 08:03:06,428] [INFO] Query marker FASTA was written to OceanDNA-b27551/markers.fasta
[2023-03-16 08:03:06,430] [INFO] Task started: Blastn
[2023-03-16 08:03:06,430] [INFO] Running command: blastn -query OceanDNA-b27551/markers.fasta -db /var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference/reference_markers.fasta -out OceanDNA-b27551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:03:07,141] [INFO] Task succeeded: Blastn
[2023-03-16 08:03:07,142] [INFO] Selected 25 target genomes.
[2023-03-16 08:03:07,142] [INFO] Target genome list was writen to OceanDNA-b27551/target_genomes.txt
[2023-03-16 08:03:07,412] [INFO] Task started: fastANI
[2023-03-16 08:03:07,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg76894d78-5a71-4c36-8f90-0401b7c5958b/OceanDNA-b27551.fa --refList OceanDNA-b27551/target_genomes.txt --output OceanDNA-b27551/fastani_result.tsv --threads 1
[2023-03-16 08:03:26,439] [INFO] Task succeeded: fastANI
[2023-03-16 08:03:26,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:03:26,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:03:26,454] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:03:26,454] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:03:26,454] [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
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.4216	491	1239	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.3178	458	1239	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.2891	358	1239	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.2859	460	1239	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	78.1307	323	1239	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.0902	386	1239	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	78.0672	329	1239	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	77.7587	274	1239	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	77.7461	324	1239	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	77.7139	309	1239	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.6263	318	1239	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5618	241	1239	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.5585	303	1239	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5095	240	1239	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.4035	238	1239	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	77.3778	207	1239	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.2883	285	1239	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.2334	242	1239	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	77.1764	188	1239	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.1317	269	1239	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.125	262	1239	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.1236	248	1239	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.0339	186	1239	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	77.0067	207	1239	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.6728	168	1239	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:03:26,455] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27551/tc_result.tsv
[2023-03-16 08:03:26,456] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:03:26,456] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:03:26,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference/checkm_data
[2023-03-16 08:03:26,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:03:26,462] [INFO] Task started: CheckM
[2023-03-16 08:03:26,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27551/checkm_input OceanDNA-b27551/checkm_result
[2023-03-16 08:04:30,386] [INFO] Task succeeded: CheckM
[2023-03-16 08:04:30,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:04:30,389] [INFO] ===== Completeness check finished =====
[2023-03-16 08:04:30,389] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:04:30,389] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27551/markers.fasta)
[2023-03-16 08:04:30,391] [INFO] Task started: Blastn
[2023-03-16 08:04:30,391] [INFO] Running command: blastn -query OceanDNA-b27551/markers.fasta -db /var/lib/cwl/stg5e23376b-fb2e-4dfc-aa5e-f6891fde3e7f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:04:31,545] [INFO] Task succeeded: Blastn
[2023-03-16 08:04:31,546] [INFO] Selected 29 target genomes.
[2023-03-16 08:04:31,546] [INFO] Target genome list was writen to OceanDNA-b27551/target_genomes_gtdb.txt
[2023-03-16 08:04:32,391] [INFO] Task started: fastANI
[2023-03-16 08:04:32,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg76894d78-5a71-4c36-8f90-0401b7c5958b/OceanDNA-b27551.fa --refList OceanDNA-b27551/target_genomes_gtdb.txt --output OceanDNA-b27551/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:04:57,540] [INFO] Task succeeded: fastANI
[2023-03-16 08:04:57,556] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:04:57,556] [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_003667315.2	s__Tropicibacter sp003667315	78.6468	451	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.6214	439	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	78.5831	464	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	78.4825	409	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	78.3554	426	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900101505.1	s__Mameliella alba	78.2936	459	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_014637725.1	s__Marivita lacus	78.2891	358	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	78.251	444	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.2163	363	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	78.1949	435	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_017255395.1	s__AWRV01 sp017255395	78.1683	403	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	78.1485	416	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_002115805.1	s__Marivita geojedonensis	78.12	324	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900100085.1	s__Salipiger marinus	78.0976	386	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_017311415.1	s__Salipiger abyssi_A	78.0669	325	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.035	353	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	78.021	333	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.9846	347	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	77.9296	323	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	77.8159	374	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_007923445.1	s__Puniceibacterium confluentis	77.7872	320	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129875.1	s__Marivita hallyeonensis	77.7701	273	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	77.7583	340	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.4802	253	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_002925845.1	s__Roseovarius nitratireducens	77.3778	207	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.2885	285	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	77.2334	242	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.1981	213	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.1491	231	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:04:57,557] [INFO] GTDB search result was written to OceanDNA-b27551/result_gtdb.tsv
[2023-03-16 08:04:57,557] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:04:57,560] [INFO] DFAST_QC result json was written to OceanDNA-b27551/dqc_result.json
[2023-03-16 08:04:57,560] [INFO] DFAST_QC completed!
[2023-03-16 08:04:57,560] [INFO] Total running time: 0h2m17s