[2023-03-16 05:09:11,163] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:11,166] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:11,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference
[2023-03-16 05:09:12,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,240] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,240] [INFO] Running command: cat /var/lib/cwl/stge4381bc8-d87d-4e50-8ee8-5dba3570fc28/OceanDNA-b30075.fa | prodigal -d OceanDNA-b30075/cds.fna -a OceanDNA-b30075/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:30,604] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:30,604] [INFO] Task started: HMMsearch
[2023-03-16 05:09:30,604] [INFO] Running command: hmmsearch --tblout OceanDNA-b30075/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference/reference_markers.hmm OceanDNA-b30075/protein.faa > /dev/null
[2023-03-16 05:09:30,799] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:30,800] [INFO] Found 6/6 markers.
[2023-03-16 05:09:30,843] [INFO] Query marker FASTA was written to OceanDNA-b30075/markers.fasta
[2023-03-16 05:09:30,844] [INFO] Task started: Blastn
[2023-03-16 05:09:30,844] [INFO] Running command: blastn -query OceanDNA-b30075/markers.fasta -db /var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference/reference_markers.fasta -out OceanDNA-b30075/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:31,662] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:31,680] [INFO] Selected 17 target genomes.
[2023-03-16 05:09:31,680] [INFO] Target genome list was writen to OceanDNA-b30075/target_genomes.txt
[2023-03-16 05:09:31,689] [INFO] Task started: fastANI
[2023-03-16 05:09:31,689] [INFO] Running command: fastANI --query /var/lib/cwl/stge4381bc8-d87d-4e50-8ee8-5dba3570fc28/OceanDNA-b30075.fa --refList OceanDNA-b30075/target_genomes.txt --output OceanDNA-b30075/fastani_result.tsv --threads 1
[2023-03-16 05:09:44,400] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:44,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:44,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:44,418] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:44,418] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:09:44,419] [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
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	87.4674	774	963	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	86.8805	786	963	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	86.3222	735	963	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	79.9271	535	963	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	79.7153	556	963	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	78.9631	406	963	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.8054	483	963	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.5276	407	963	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.1628	353	963	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.1154	371	963	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.61	288	963	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	77.4562	265	963	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.2461	228	963	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.201	244	963	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.0692	197	963	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0484	221	963	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.9853	245	963	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:09:44,422] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30075/tc_result.tsv
[2023-03-16 05:09:44,429] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:44,429] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:44,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference/checkm_data
[2023-03-16 05:09:44,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:44,450] [INFO] Task started: CheckM
[2023-03-16 05:09:44,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30075/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30075/checkm_input OceanDNA-b30075/checkm_result
[2023-03-16 05:10:33,242] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:33,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:33,455] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:33,455] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:33,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30075/markers.fasta)
[2023-03-16 05:10:33,456] [INFO] Task started: Blastn
[2023-03-16 05:10:33,456] [INFO] Running command: blastn -query OceanDNA-b30075/markers.fasta -db /var/lib/cwl/stg926268b1-42fe-46bf-9c3a-43f0dd11ac73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30075/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:35,101] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:35,105] [INFO] Selected 15 target genomes.
[2023-03-16 05:10:35,105] [INFO] Target genome list was writen to OceanDNA-b30075/target_genomes_gtdb.txt
[2023-03-16 05:10:35,127] [INFO] Task started: fastANI
[2023-03-16 05:10:35,127] [INFO] Running command: fastANI --query /var/lib/cwl/stge4381bc8-d87d-4e50-8ee8-5dba3570fc28/OceanDNA-b30075.fa --refList OceanDNA-b30075/target_genomes_gtdb.txt --output OceanDNA-b30075/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:46,505] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:46,514] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:10:46,514] [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_900172365.1	s__Roseovarius gaetbuli	87.4674	774	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142625.1	s__Roseovarius marisflavi	86.8805	786	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	86.3222	735	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109455.1	s__Roseovarius azorensis	79.9216	536	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	79.7152	556	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_000744325.1	s__Roseovarius sp000744325	79.5822	557	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066915.1	s__Roseovarius sp018066915	79.5724	511	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_000152845.1	s__Roseovarius sp000152845	79.2329	529	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.99	97.99	0.83	0.83	2	-
GCF_002080415.1	s__Roseovarius mucosus_A	79.2167	517	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_000152625.1	s__Roseovarius nubinhibens	78.5232	408	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_003072125.1	s__Roseovarius sediminicola	78.1734	352	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.1209	371	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	77.803	356	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	77.7761	331	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	77.2199	231	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:46,517] [INFO] GTDB search result was written to OceanDNA-b30075/result_gtdb.tsv
[2023-03-16 05:10:46,517] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:46,522] [INFO] DFAST_QC result json was written to OceanDNA-b30075/dqc_result.json
[2023-03-16 05:10:46,522] [INFO] DFAST_QC completed!
[2023-03-16 05:10:46,522] [INFO] Total running time: 0h1m35s