[2023-03-16 23:05:03,896] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,896] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,896] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference
[2023-03-16 23:05:05,121] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,121] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,121] [INFO] Running command: cat /var/lib/cwl/stg7b762bee-6d9c-491c-bef9-7ed97e930865/OceanDNA-b32934.fa | prodigal -d OceanDNA-b32934/cds.fna -a OceanDNA-b32934/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:26,017] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:26,018] [INFO] Task started: HMMsearch
[2023-03-16 23:05:26,018] [INFO] Running command: hmmsearch --tblout OceanDNA-b32934/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference/reference_markers.hmm OceanDNA-b32934/protein.faa > /dev/null
[2023-03-16 23:05:26,284] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:26,285] [INFO] Found 6/6 markers.
[2023-03-16 23:05:26,307] [INFO] Query marker FASTA was written to OceanDNA-b32934/markers.fasta
[2023-03-16 23:05:26,308] [INFO] Task started: Blastn
[2023-03-16 23:05:26,308] [INFO] Running command: blastn -query OceanDNA-b32934/markers.fasta -db /var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference/reference_markers.fasta -out OceanDNA-b32934/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:27,021] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:27,022] [INFO] Selected 27 target genomes.
[2023-03-16 23:05:27,022] [INFO] Target genome list was writen to OceanDNA-b32934/target_genomes.txt
[2023-03-16 23:05:27,036] [INFO] Task started: fastANI
[2023-03-16 23:05:27,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b762bee-6d9c-491c-bef9-7ed97e930865/OceanDNA-b32934.fa --refList OceanDNA-b32934/target_genomes.txt --output OceanDNA-b32934/fastani_result.tsv --threads 1
[2023-03-16 23:05:48,299] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:48,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:48,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:48,309] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:48,309] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:48,309] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.7974	69	1097	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.7293	57	1097	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.623	67	1097	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.6042	103	1097	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.5946	72	1097	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.5588	78	1097	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.5141	84	1097	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.5036	85	1097	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.3801	53	1097	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.3374	61	1097	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.124	73	1097	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.0893	71	1097	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.0607	61	1097	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.0352	60	1097	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.9949	64	1097	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:48,309] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32934/tc_result.tsv
[2023-03-16 23:05:48,310] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:48,310] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:48,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference/checkm_data
[2023-03-16 23:05:48,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:48,315] [INFO] Task started: CheckM
[2023-03-16 23:05:48,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32934/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32934/checkm_input OceanDNA-b32934/checkm_result
[2023-03-16 23:06:41,158] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:41,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:41,163] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:41,163] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:41,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32934/markers.fasta)
[2023-03-16 23:06:41,164] [INFO] Task started: Blastn
[2023-03-16 23:06:41,164] [INFO] Running command: blastn -query OceanDNA-b32934/markers.fasta -db /var/lib/cwl/stgf0f2f779-2ad7-4679-b2c0-54b9a304935c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32934/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:42,514] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:42,515] [INFO] Selected 24 target genomes.
[2023-03-16 23:06:42,515] [INFO] Target genome list was writen to OceanDNA-b32934/target_genomes_gtdb.txt
[2023-03-16 23:06:43,531] [INFO] Task started: fastANI
[2023-03-16 23:06:43,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b762bee-6d9c-491c-bef9-7ed97e930865/OceanDNA-b32934.fa --refList OceanDNA-b32934/target_genomes_gtdb.txt --output OceanDNA-b32934/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:57,028] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:57,038] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:57,038] [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_002937555.1	s__PTKB01 sp002937555	82.3367	541	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	79.4784	596	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002717225.1	s__PTKB01 sp002717225	76.497	147	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523425.1	s__WTGU01 sp011523425	76.259	154	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	75.7768	70	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.623	67	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	75.5588	78	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	75.4914	57	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCA_903941105.1	s__CAJANL01 sp903941105	75.4346	57	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	75.4228	55	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	75.3586	66	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_902826565.1	s__CADEFF01 sp902826565	75.3055	67	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108475.1	s__Phaeospirillum fulvum_A	75.3045	50	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	75.2931	60	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185205.1	s__Pseudolabrys sp016185205	75.287	60	1097	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:57,038] [INFO] GTDB search result was written to OceanDNA-b32934/result_gtdb.tsv
[2023-03-16 23:06:57,038] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:57,040] [INFO] DFAST_QC result json was written to OceanDNA-b32934/dqc_result.json
[2023-03-16 23:06:57,040] [INFO] DFAST_QC completed!
[2023-03-16 23:06:57,040] [INFO] Total running time: 0h1m53s