[2023-03-15 17:39:54,931] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:39:54,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:39:54,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference
[2023-03-15 17:39:57,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:39:57,563] [INFO] Task started: Prodigal
[2023-03-15 17:39:57,563] [INFO] Running command: cat /var/lib/cwl/stg3f75c0dc-b366-4325-a1fc-c55bde134242/OceanDNA-b27550.fa | prodigal -d OceanDNA-b27550/cds.fna -a OceanDNA-b27550/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:40:08,983] [INFO] Task succeeded: Prodigal
[2023-03-15 17:40:08,983] [INFO] Task started: HMMsearch
[2023-03-15 17:40:08,983] [INFO] Running command: hmmsearch --tblout OceanDNA-b27550/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference/reference_markers.hmm OceanDNA-b27550/protein.faa > /dev/null
[2023-03-15 17:40:09,144] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:40:09,145] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3f75c0dc-b366-4325-a1fc-c55bde134242/OceanDNA-b27550.fa]
[2023-03-15 17:40:09,163] [INFO] Query marker FASTA was written to OceanDNA-b27550/markers.fasta
[2023-03-15 17:40:09,164] [INFO] Task started: Blastn
[2023-03-15 17:40:09,164] [INFO] Running command: blastn -query OceanDNA-b27550/markers.fasta -db /var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference/reference_markers.fasta -out OceanDNA-b27550/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:09,682] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:09,682] [INFO] Selected 13 target genomes.
[2023-03-15 17:40:09,683] [INFO] Target genome list was writen to OceanDNA-b27550/target_genomes.txt
[2023-03-15 17:40:09,720] [INFO] Task started: fastANI
[2023-03-15 17:40:09,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f75c0dc-b366-4325-a1fc-c55bde134242/OceanDNA-b27550.fa --refList OceanDNA-b27550/target_genomes.txt --output OceanDNA-b27550/fastani_result.tsv --threads 1
[2023-03-15 17:40:18,188] [INFO] Task succeeded: fastANI
[2023-03-15 17:40:18,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:40:18,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:40:18,197] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:40:18,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:40:18,197] [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
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.7924	195	535	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.7635	166	535	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.5889	188	535	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.1689	140	535	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.0611	148	535	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.0551	149	535	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.02	141	535	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	76.9956	138	535	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.7494	86	535	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7217	105	535	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6796	88	535	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6283	74	535	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:40:18,198] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27550/tc_result.tsv
[2023-03-15 17:40:18,198] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:40:18,198] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:40:18,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference/checkm_data
[2023-03-15 17:40:18,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:40:18,220] [INFO] Task started: CheckM
[2023-03-15 17:40:18,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27550/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27550/checkm_input OceanDNA-b27550/checkm_result
[2023-03-15 17:40:50,990] [INFO] Task succeeded: CheckM
[2023-03-15 17:40:50,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:40:50,992] [INFO] ===== Completeness check finished =====
[2023-03-15 17:40:50,992] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:40:50,993] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27550/markers.fasta)
[2023-03-15 17:40:50,994] [INFO] Task started: Blastn
[2023-03-15 17:40:50,994] [INFO] Running command: blastn -query OceanDNA-b27550/markers.fasta -db /var/lib/cwl/stg7ac43684-8c0d-4a4d-9a4a-5a3c0768b081/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27550/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:51,668] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:51,669] [INFO] Selected 13 target genomes.
[2023-03-15 17:40:51,669] [INFO] Target genome list was writen to OceanDNA-b27550/target_genomes_gtdb.txt
[2023-03-15 17:40:51,814] [INFO] Task started: fastANI
[2023-03-15 17:40:51,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f75c0dc-b366-4325-a1fc-c55bde134242/OceanDNA-b27550.fa --refList OceanDNA-b27550/target_genomes_gtdb.txt --output OceanDNA-b27550/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:41:00,428] [INFO] Task succeeded: fastANI
[2023-03-15 17:41:00,436] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:41:00,437] [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_016888515.1	s__Shimia_A biformata	78.2475	175	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.0238	190	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	77.791	161	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.7832	165	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.5889	188	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.4083	109	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	77.3797	141	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.2382	180	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.1689	140	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032095.1	s__Ruegeria atlantica_E	77.0749	89	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	77.0611	148	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900101505.1	s__Mameliella alba	77.02	141	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_001650895.1	s__EhC02 sp001650895	76.8848	134	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:41:00,437] [INFO] GTDB search result was written to OceanDNA-b27550/result_gtdb.tsv
[2023-03-15 17:41:00,437] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:41:00,438] [INFO] DFAST_QC result json was written to OceanDNA-b27550/dqc_result.json
[2023-03-15 17:41:00,439] [INFO] DFAST_QC completed!
[2023-03-15 17:41:00,439] [INFO] Total running time: 0h1m6s