[2023-03-16 03:47:32,868] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,868] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,868] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference
[2023-03-16 03:47:34,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,535] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,535] [INFO] Running command: cat /var/lib/cwl/stg3a267171-0919-4651-b42a-7a97c6604093/OceanDNA-b30769.fa | prodigal -d OceanDNA-b30769/cds.fna -a OceanDNA-b30769/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:44,682] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:44,682] [INFO] Task started: HMMsearch
[2023-03-16 03:47:44,682] [INFO] Running command: hmmsearch --tblout OceanDNA-b30769/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference/reference_markers.hmm OceanDNA-b30769/protein.faa > /dev/null
[2023-03-16 03:47:44,913] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:44,914] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3a267171-0919-4651-b42a-7a97c6604093/OceanDNA-b30769.fa]
[2023-03-16 03:47:44,932] [INFO] Query marker FASTA was written to OceanDNA-b30769/markers.fasta
[2023-03-16 03:47:44,933] [INFO] Task started: Blastn
[2023-03-16 03:47:44,933] [INFO] Running command: blastn -query OceanDNA-b30769/markers.fasta -db /var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference/reference_markers.fasta -out OceanDNA-b30769/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:45,561] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:45,562] [INFO] Selected 30 target genomes.
[2023-03-16 03:47:45,562] [INFO] Target genome list was writen to OceanDNA-b30769/target_genomes.txt
[2023-03-16 03:47:45,581] [INFO] Task started: fastANI
[2023-03-16 03:47:45,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a267171-0919-4651-b42a-7a97c6604093/OceanDNA-b30769.fa --refList OceanDNA-b30769/target_genomes.txt --output OceanDNA-b30769/fastani_result.tsv --threads 1
[2023-03-16 03:48:13,095] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:13,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:13,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:13,103] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:13,104] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:13,104] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.6359	65	469	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0756	65	469	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.0688	58	469	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.0457	59	469	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.7406	64	469	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.7328	54	469	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.6712	53	469	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.6415	51	469	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.6267	58	469	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.6133	57	469	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	75.5116	55	469	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.3272	67	469	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:13,104] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30769/tc_result.tsv
[2023-03-16 03:48:13,104] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:13,104] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:13,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference/checkm_data
[2023-03-16 03:48:13,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:13,340] [INFO] Task started: CheckM
[2023-03-16 03:48:13,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30769/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30769/checkm_input OceanDNA-b30769/checkm_result
[2023-03-16 03:48:42,775] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:42,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.73%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:42,778] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:42,778] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:42,778] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30769/markers.fasta)
[2023-03-16 03:48:42,778] [INFO] Task started: Blastn
[2023-03-16 03:48:42,778] [INFO] Running command: blastn -query OceanDNA-b30769/markers.fasta -db /var/lib/cwl/stgaa24bfdc-88ec-4415-8dad-3f5c47ffa471/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30769/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:43,788] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:43,789] [INFO] Selected 21 target genomes.
[2023-03-16 03:48:43,789] [INFO] Target genome list was writen to OceanDNA-b30769/target_genomes_gtdb.txt
[2023-03-16 03:48:43,869] [INFO] Task started: fastANI
[2023-03-16 03:48:43,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a267171-0919-4651-b42a-7a97c6604093/OceanDNA-b30769.fa --refList OceanDNA-b30769/target_genomes_gtdb.txt --output OceanDNA-b30769/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:56,483] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:56,491] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:56,491] [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_002686255.1	s__Casp-alpha2 sp002686255	76.6444	65	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.4876	52	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.4775	79	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	76.3232	52	469	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	-
GCF_900230255.1	s__Caenispirillum bisanense	76.1942	70	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.1791	65	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.1006	53	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.0713	69	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901915.1	s__Phaeospirillum sp903901915	75.9326	55	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.99	99.99	0.95	0.95	2	-
GCF_014197795.1	s__Rhodospira goensis	75.9109	53	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	75.6506	54	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009377375.1	s__WHUE01 sp009377375	75.4523	53	469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:56,491] [INFO] GTDB search result was written to OceanDNA-b30769/result_gtdb.tsv
[2023-03-16 03:48:56,491] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:56,493] [INFO] DFAST_QC result json was written to OceanDNA-b30769/dqc_result.json
[2023-03-16 03:48:56,493] [INFO] DFAST_QC completed!
[2023-03-16 03:48:56,493] [INFO] Total running time: 0h1m24s