[2023-03-18 07:54:29,664] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,665] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,665] [INFO] DQC Reference Directory: /var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference
[2023-03-18 07:54:30,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,760] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,760] [INFO] Running command: cat /var/lib/cwl/stgcbada671-2aec-4cfb-9994-6f1213cb2ea9/OceanDNA-b23915.fa | prodigal -d OceanDNA-b23915/cds.fna -a OceanDNA-b23915/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:47,151] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:47,151] [INFO] Task started: HMMsearch
[2023-03-18 07:54:47,151] [INFO] Running command: hmmsearch --tblout OceanDNA-b23915/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference/reference_markers.hmm OceanDNA-b23915/protein.faa > /dev/null
[2023-03-18 07:54:47,346] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:47,347] [INFO] Found 6/6 markers.
[2023-03-18 07:54:47,367] [INFO] Query marker FASTA was written to OceanDNA-b23915/markers.fasta
[2023-03-18 07:54:47,368] [INFO] Task started: Blastn
[2023-03-18 07:54:47,369] [INFO] Running command: blastn -query OceanDNA-b23915/markers.fasta -db /var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference/reference_markers.fasta -out OceanDNA-b23915/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:48,067] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:48,069] [INFO] Selected 20 target genomes.
[2023-03-18 07:54:48,069] [INFO] Target genome list was writen to OceanDNA-b23915/target_genomes.txt
[2023-03-18 07:54:48,080] [INFO] Task started: fastANI
[2023-03-18 07:54:48,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbada671-2aec-4cfb-9994-6f1213cb2ea9/OceanDNA-b23915.fa --refList OceanDNA-b23915/target_genomes.txt --output OceanDNA-b23915/fastani_result.tsv --threads 1
[2023-03-18 07:54:59,063] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:59,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:59,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:59,083] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 07:54:59,083] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:54:59,083] [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
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	97.4655	763	878	95	conclusive
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	77.4931	215	878	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	77.3771	217	878	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	77.352	206	878	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.3024	162	878	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.2515	166	878	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.2445	153	878	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.2122	156	878	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.2122	156	878	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.1722	156	878	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.1469	156	878	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.8121	150	878	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	76.2705	70	878	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	75.9763	56	878	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	75.8313	70	878	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	75.2815	61	878	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:54:59,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23915/tc_result.tsv
[2023-03-18 07:54:59,084] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:59,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:59,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference/checkm_data
[2023-03-18 07:54:59,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:59,091] [INFO] Task started: CheckM
[2023-03-18 07:54:59,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23915/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23915/checkm_input OceanDNA-b23915/checkm_result
[2023-03-18 07:55:43,003] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:43,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:43,005] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:43,006] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:43,006] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23915/markers.fasta)
[2023-03-18 07:55:43,007] [INFO] Task started: Blastn
[2023-03-18 07:55:43,007] [INFO] Running command: blastn -query OceanDNA-b23915/markers.fasta -db /var/lib/cwl/stgb54f3e16-f617-4486-b08d-f638e06712c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23915/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:44,281] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:44,282] [INFO] Selected 12 target genomes.
[2023-03-18 07:55:44,282] [INFO] Target genome list was writen to OceanDNA-b23915/target_genomes_gtdb.txt
[2023-03-18 07:55:44,327] [INFO] Task started: fastANI
[2023-03-18 07:55:44,327] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbada671-2aec-4cfb-9994-6f1213cb2ea9/OceanDNA-b23915.fa --refList OceanDNA-b23915/target_genomes_gtdb.txt --output OceanDNA-b23915/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:51,312] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:51,320] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:55:51,320] [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_003129605.1	s__Hyphobacterium indicum	97.4353	764	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016124665.1	s__Hyphobacterium sp016124665	94.779	739	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783385.1	s__Hyphobacterium sp002783385	85.5385	565	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323565.1	s__Hyphobacterium sp014323565	83.677	630	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124205.1	s__Hyphobacterium sp016124205	77.8633	218	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692855.1	s__Hyphobacterium sp002692855	77.597	241	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCA_017642925.1	s__Maricaulis sp017642925	77.5346	230	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	77.4961	214	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_005871165.1	s__Maricaulis sp005871165	77.3771	217	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	77.3231	166	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_016817355.1	s__Maricaulis parjimensis	77.263	214	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	77.2122	156	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:51,320] [INFO] GTDB search result was written to OceanDNA-b23915/result_gtdb.tsv
[2023-03-18 07:55:51,320] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:51,322] [INFO] DFAST_QC result json was written to OceanDNA-b23915/dqc_result.json
[2023-03-18 07:55:51,322] [INFO] DFAST_QC completed!
[2023-03-18 07:55:51,322] [INFO] Total running time: 0h1m22s