[2023-03-16 08:30:41,130] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:30:41,130] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:30:41,130] [INFO] DQC Reference Directory: /var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference
[2023-03-16 08:30:43,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:30:43,994] [INFO] Task started: Prodigal
[2023-03-16 08:30:43,994] [INFO] Running command: cat /var/lib/cwl/stgf6ca3c92-7bf8-4ded-94c3-9193867f916d/OceanDNA-b6436.fa | prodigal -d OceanDNA-b6436/cds.fna -a OceanDNA-b6436/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:31:06,786] [INFO] Task succeeded: Prodigal
[2023-03-16 08:31:06,786] [INFO] Task started: HMMsearch
[2023-03-16 08:31:06,786] [INFO] Running command: hmmsearch --tblout OceanDNA-b6436/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference/reference_markers.hmm OceanDNA-b6436/protein.faa > /dev/null
[2023-03-16 08:31:07,002] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:31:07,003] [INFO] Found 6/6 markers.
[2023-03-16 08:31:07,026] [INFO] Query marker FASTA was written to OceanDNA-b6436/markers.fasta
[2023-03-16 08:31:07,027] [INFO] Task started: Blastn
[2023-03-16 08:31:07,027] [INFO] Running command: blastn -query OceanDNA-b6436/markers.fasta -db /var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference/reference_markers.fasta -out OceanDNA-b6436/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:31:07,624] [INFO] Task succeeded: Blastn
[2023-03-16 08:31:07,628] [INFO] Selected 12 target genomes.
[2023-03-16 08:31:07,628] [INFO] Target genome list was writen to OceanDNA-b6436/target_genomes.txt
[2023-03-16 08:31:07,649] [INFO] Task started: fastANI
[2023-03-16 08:31:07,649] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6ca3c92-7bf8-4ded-94c3-9193867f916d/OceanDNA-b6436.fa --refList OceanDNA-b6436/target_genomes.txt --output OceanDNA-b6436/fastani_result.tsv --threads 1
[2023-03-16 08:31:15,596] [INFO] Task succeeded: fastANI
[2023-03-16 08:31:15,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:31:15,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:31:15,632] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:31:15,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:31:15,632] [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
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	90.6644	845	1010	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	85.5571	786	1010	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	85.3286	790	1010	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	83.1338	687	1010	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	80.9373	681	1010	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.7179	678	1010	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.7595	595	1010	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	78.6663	353	1010	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.7414	123	1010	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.7407	162	1010	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:31:15,633] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6436/tc_result.tsv
[2023-03-16 08:31:15,635] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:31:15,636] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:31:15,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference/checkm_data
[2023-03-16 08:31:15,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:31:15,642] [INFO] Task started: CheckM
[2023-03-16 08:31:15,642] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6436/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6436/checkm_input OceanDNA-b6436/checkm_result
[2023-03-16 08:32:14,270] [INFO] Task succeeded: CheckM
[2023-03-16 08:32:14,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:32:14,273] [INFO] ===== Completeness check finished =====
[2023-03-16 08:32:14,273] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:32:14,273] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6436/markers.fasta)
[2023-03-16 08:32:14,274] [INFO] Task started: Blastn
[2023-03-16 08:32:14,274] [INFO] Running command: blastn -query OceanDNA-b6436/markers.fasta -db /var/lib/cwl/stge30602a2-81d8-46d5-9945-97ade4e4174f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6436/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:32:15,069] [INFO] Task succeeded: Blastn
[2023-03-16 08:32:15,070] [INFO] Selected 8 target genomes.
[2023-03-16 08:32:15,070] [INFO] Target genome list was writen to OceanDNA-b6436/target_genomes_gtdb.txt
[2023-03-16 08:32:15,086] [INFO] Task started: fastANI
[2023-03-16 08:32:15,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6ca3c92-7bf8-4ded-94c3-9193867f916d/OceanDNA-b6436.fa --refList OceanDNA-b6436/target_genomes_gtdb.txt --output OceanDNA-b6436/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:32:21,145] [INFO] Task succeeded: fastANI
[2023-03-16 08:32:21,151] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:32:21,151] [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_002364215.1	s__Aequorivita sp002364215	99.9913	1000	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	conclusive
GCF_001573155.1	s__Aequorivita aquimaris	90.674	844	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	87.1529	749	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_016757735.1	s__Aequorivita sp016757735	85.5484	787	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	85.348	773	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	85.3147	791	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_001641085.1	s__Aequorivita soesokkakensis	83.1464	686	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_007997135.1	s__Aequorivita lipolytica	80.7364	676	1010	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:32:21,151] [INFO] GTDB search result was written to OceanDNA-b6436/result_gtdb.tsv
[2023-03-16 08:32:21,151] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:32:21,153] [INFO] DFAST_QC result json was written to OceanDNA-b6436/dqc_result.json
[2023-03-16 08:32:21,153] [INFO] DFAST_QC completed!
[2023-03-16 08:32:21,154] [INFO] Total running time: 0h1m40s