[2023-03-14 13:37:57,148] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:37:57,148] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:37:57,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference
[2023-03-14 13:37:58,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:37:58,249] [INFO] Task started: Prodigal
[2023-03-14 13:37:58,249] [INFO] Running command: cat /var/lib/cwl/stg521f5ddb-231f-4256-9743-1837d0198b54/OceanDNA-b38355.fa | prodigal -d OceanDNA-b38355/cds.fna -a OceanDNA-b38355/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:38:21,603] [INFO] Task succeeded: Prodigal
[2023-03-14 13:38:21,604] [INFO] Task started: HMMsearch
[2023-03-14 13:38:21,604] [INFO] Running command: hmmsearch --tblout OceanDNA-b38355/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference/reference_markers.hmm OceanDNA-b38355/protein.faa > /dev/null
[2023-03-14 13:38:21,864] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:38:21,865] [INFO] Found 6/6 markers.
[2023-03-14 13:38:21,890] [INFO] Query marker FASTA was written to OceanDNA-b38355/markers.fasta
[2023-03-14 13:38:21,891] [INFO] Task started: Blastn
[2023-03-14 13:38:21,891] [INFO] Running command: blastn -query OceanDNA-b38355/markers.fasta -db /var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference/reference_markers.fasta -out OceanDNA-b38355/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:22,622] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:22,623] [INFO] Selected 17 target genomes.
[2023-03-14 13:38:22,623] [INFO] Target genome list was writen to OceanDNA-b38355/target_genomes.txt
[2023-03-14 13:38:22,632] [INFO] Task started: fastANI
[2023-03-14 13:38:22,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg521f5ddb-231f-4256-9743-1837d0198b54/OceanDNA-b38355.fa --refList OceanDNA-b38355/target_genomes.txt --output OceanDNA-b38355/fastani_result.tsv --threads 1
[2023-03-14 13:38:36,813] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:36,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:38:36,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:38:36,824] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:38:36,824] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:38:36,824] [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
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	90.6477	1120	1283	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	90.441	1106	1283	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	85.7059	990	1283	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	85.7027	996	1283	95	below_threshold
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	85.4845	929	1283	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	84.8247	948	1283	95	below_threshold
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	83.4	954	1283	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	82.7748	873	1283	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	82.6051	865	1283	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.1566	421	1283	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.0858	394	1283	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.9475	385	1283	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.909	406	1283	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	78.6339	366	1283	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	78.2554	394	1283	95	below_threshold
Halomonas endophytica	strain=MC28	GCA_002879615.1	2033802	2033802	type	True	78.0058	310	1283	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	77.5431	269	1283	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:38:36,824] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38355/tc_result.tsv
[2023-03-14 13:38:36,824] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:38:36,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:38:36,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference/checkm_data
[2023-03-14 13:38:36,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:38:36,831] [INFO] Task started: CheckM
[2023-03-14 13:38:36,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38355/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38355/checkm_input OceanDNA-b38355/checkm_result
[2023-03-14 13:39:57,591] [INFO] Task succeeded: CheckM
[2023-03-14 13:39:57,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:39:57,599] [INFO] ===== Completeness check finished =====
[2023-03-14 13:39:57,599] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:39:57,600] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38355/markers.fasta)
[2023-03-14 13:39:57,601] [INFO] Task started: Blastn
[2023-03-14 13:39:57,601] [INFO] Running command: blastn -query OceanDNA-b38355/markers.fasta -db /var/lib/cwl/stg5b6426a0-05ce-40d5-ba07-bad201ff86b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38355/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:39:59,425] [INFO] Task succeeded: Blastn
[2023-03-14 13:39:59,428] [INFO] Selected 10 target genomes.
[2023-03-14 13:39:59,428] [INFO] Target genome list was writen to OceanDNA-b38355/target_genomes_gtdb.txt
[2023-03-14 13:39:59,434] [INFO] Task started: fastANI
[2023-03-14 13:39:59,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg521f5ddb-231f-4256-9743-1837d0198b54/OceanDNA-b38355.fa --refList OceanDNA-b38355/target_genomes_gtdb.txt --output OceanDNA-b38355/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:40:10,455] [INFO] Task succeeded: fastANI
[2023-03-14 13:40:10,462] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:40:10,462] [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_002695065.1	s__Salinicola sp002695065	99.8975	1220	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	conclusive
GCF_008298015.1	s__Salinicola sp008298015	94.2253	1105	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206045.1	s__Salinicola lusitanus	90.6477	1120	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206615.1	s__Salinicola acroporae	90.441	1106	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001937195.1	s__Salinicola socius	85.672	993	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_003206135.1	s__Salinicola salarius	85.4845	929	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCF_002179555.1	s__Salinicola salarius_A	85.3436	902	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206065.1	s__Salinicola halimionae	83.4	954	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206715.1	s__Salinicola peritrichatus	82.5869	867	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754225.1	s__Cobetia amphilecti	78.2403	310	1283	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
--------------------------------------------------------------------------------
[2023-03-14 13:40:10,463] [INFO] GTDB search result was written to OceanDNA-b38355/result_gtdb.tsv
[2023-03-14 13:40:10,464] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:40:10,467] [INFO] DFAST_QC result json was written to OceanDNA-b38355/dqc_result.json
[2023-03-14 13:40:10,467] [INFO] DFAST_QC completed!
[2023-03-14 13:40:10,467] [INFO] Total running time: 0h2m13s