[2023-03-15 13:20:51,559] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,559] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference
[2023-03-15 13:20:52,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,674] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,674] [INFO] Running command: cat /var/lib/cwl/stgb28cc2d1-6b95-4b58-9ab7-03859021ae79/OceanDNA-b29555.fa | prodigal -d OceanDNA-b29555/cds.fna -a OceanDNA-b29555/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:13,784] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:13,784] [INFO] Task started: HMMsearch
[2023-03-15 13:21:13,784] [INFO] Running command: hmmsearch --tblout OceanDNA-b29555/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference/reference_markers.hmm OceanDNA-b29555/protein.faa > /dev/null
[2023-03-15 13:21:14,104] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:14,104] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb28cc2d1-6b95-4b58-9ab7-03859021ae79/OceanDNA-b29555.fa]
[2023-03-15 13:21:14,127] [INFO] Query marker FASTA was written to OceanDNA-b29555/markers.fasta
[2023-03-15 13:21:14,128] [INFO] Task started: Blastn
[2023-03-15 13:21:14,128] [INFO] Running command: blastn -query OceanDNA-b29555/markers.fasta -db /var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference/reference_markers.fasta -out OceanDNA-b29555/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:14,867] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:14,868] [INFO] Selected 13 target genomes.
[2023-03-15 13:21:14,868] [INFO] Target genome list was writen to OceanDNA-b29555/target_genomes.txt
[2023-03-15 13:21:14,883] [INFO] Task started: fastANI
[2023-03-15 13:21:14,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28cc2d1-6b95-4b58-9ab7-03859021ae79/OceanDNA-b29555.fa --refList OceanDNA-b29555/target_genomes.txt --output OceanDNA-b29555/fastani_result.tsv --threads 1
[2023-03-15 13:21:25,589] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:25,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:25,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:25,598] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:21:25,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:21:25,598] [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
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	97.355	953	1082	95	conclusive
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	92.1616	990	1082	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	81.4645	702	1082	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6534	402	1082	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.3068	397	1082	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	78.0094	382	1082	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.8588	376	1082	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.85	321	1082	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.8304	322	1082	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.7627	340	1082	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.6548	364	1082	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.3502	281	1082	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.3174	269	1082	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:25,599] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29555/tc_result.tsv
[2023-03-15 13:21:25,599] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:25,599] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:25,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference/checkm_data
[2023-03-15 13:21:25,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:25,605] [INFO] Task started: CheckM
[2023-03-15 13:21:25,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29555/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29555/checkm_input OceanDNA-b29555/checkm_result
[2023-03-15 13:22:18,380] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:18,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:18,384] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:18,384] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:18,384] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29555/markers.fasta)
[2023-03-15 13:22:18,385] [INFO] Task started: Blastn
[2023-03-15 13:22:18,385] [INFO] Running command: blastn -query OceanDNA-b29555/markers.fasta -db /var/lib/cwl/stg15a716db-ec87-4caa-ae4b-c641dd907620/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29555/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:19,570] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:19,571] [INFO] Selected 9 target genomes.
[2023-03-15 13:22:19,571] [INFO] Target genome list was writen to OceanDNA-b29555/target_genomes_gtdb.txt
[2023-03-15 13:22:19,581] [INFO] Task started: fastANI
[2023-03-15 13:22:19,581] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28cc2d1-6b95-4b58-9ab7-03859021ae79/OceanDNA-b29555.fa --refList OceanDNA-b29555/target_genomes_gtdb.txt --output OceanDNA-b29555/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:27,202] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:27,208] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:27,208] [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_001879695.1	s__Nioella sediminis	97.355	953	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_004000255.1	s__Nioella ostreopsis	92.1616	990	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	81.4643	702	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	81.1579	651	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	80.6691	500	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	80.2184	647	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_000590925.1	s__Roseicyclus elongatus	78.6434	403	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	77.8214	322	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_004342445.1	s__Rhodovulum euryhalinum	77.7625	340	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:27,209] [INFO] GTDB search result was written to OceanDNA-b29555/result_gtdb.tsv
[2023-03-15 13:22:27,209] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:27,211] [INFO] DFAST_QC result json was written to OceanDNA-b29555/dqc_result.json
[2023-03-15 13:22:27,211] [INFO] DFAST_QC completed!
[2023-03-15 13:22:27,211] [INFO] Total running time: 0h1m36s