[2023-03-17 03:29:19,769] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:29:19,769] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:29:19,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference
[2023-03-17 03:29:21,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:29:21,321] [INFO] Task started: Prodigal
[2023-03-17 03:29:21,322] [INFO] Running command: cat /var/lib/cwl/stg4fa6c12b-9b03-41ac-b78f-6863cb134173/OceanDNA-b30154.fa | prodigal -d OceanDNA-b30154/cds.fna -a OceanDNA-b30154/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:29:46,200] [INFO] Task succeeded: Prodigal
[2023-03-17 03:29:46,200] [INFO] Task started: HMMsearch
[2023-03-17 03:29:46,200] [INFO] Running command: hmmsearch --tblout OceanDNA-b30154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference/reference_markers.hmm OceanDNA-b30154/protein.faa > /dev/null
[2023-03-17 03:29:46,409] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:29:46,409] [INFO] Found 6/6 markers.
[2023-03-17 03:29:46,434] [INFO] Query marker FASTA was written to OceanDNA-b30154/markers.fasta
[2023-03-17 03:29:46,434] [INFO] Task started: Blastn
[2023-03-17 03:29:46,434] [INFO] Running command: blastn -query OceanDNA-b30154/markers.fasta -db /var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference/reference_markers.fasta -out OceanDNA-b30154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:47,041] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:47,042] [INFO] Selected 22 target genomes.
[2023-03-17 03:29:47,042] [INFO] Target genome list was writen to OceanDNA-b30154/target_genomes.txt
[2023-03-17 03:29:47,052] [INFO] Task started: fastANI
[2023-03-17 03:29:47,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fa6c12b-9b03-41ac-b78f-6863cb134173/OceanDNA-b30154.fa --refList OceanDNA-b30154/target_genomes.txt --output OceanDNA-b30154/fastani_result.tsv --threads 1
[2023-03-17 03:30:01,846] [INFO] Task succeeded: fastANI
[2023-03-17 03:30:01,846] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:30:01,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:30:01,857] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:30:01,857] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:30:01,857] [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
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	79.5727	565	1253	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	79.5398	556	1253	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	78.961	464	1253	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	78.2391	365	1253	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.5503	215	1253	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	77.5427	217	1253	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.4715	178	1253	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.3658	297	1253	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	77.3463	292	1253	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	77.3144	228	1253	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.3071	242	1253	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	77.1849	186	1253	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.005	216	1253	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.2319	149	1253	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.1928	107	1253	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.1803	108	1253	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	76.132	114	1253	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	75.7421	97	1253	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	75.7288	73	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:30:01,857] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30154/tc_result.tsv
[2023-03-17 03:30:01,857] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:30:01,857] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:30:01,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference/checkm_data
[2023-03-17 03:30:01,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:30:01,863] [INFO] Task started: CheckM
[2023-03-17 03:30:01,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30154/checkm_input OceanDNA-b30154/checkm_result
[2023-03-17 03:31:04,803] [INFO] Task succeeded: CheckM
[2023-03-17 03:31:04,804] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:31:04,806] [INFO] ===== Completeness check finished =====
[2023-03-17 03:31:04,806] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:31:04,806] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30154/markers.fasta)
[2023-03-17 03:31:04,807] [INFO] Task started: Blastn
[2023-03-17 03:31:04,807] [INFO] Running command: blastn -query OceanDNA-b30154/markers.fasta -db /var/lib/cwl/stgcddd6516-84c7-49fe-a696-faa1d1f3e4fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:31:05,720] [INFO] Task succeeded: Blastn
[2023-03-17 03:31:05,721] [INFO] Selected 13 target genomes.
[2023-03-17 03:31:05,721] [INFO] Target genome list was writen to OceanDNA-b30154/target_genomes_gtdb.txt
[2023-03-17 03:31:05,755] [INFO] Task started: fastANI
[2023-03-17 03:31:05,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fa6c12b-9b03-41ac-b78f-6863cb134173/OceanDNA-b30154.fa --refList OceanDNA-b30154/target_genomes_gtdb.txt --output OceanDNA-b30154/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:31:15,178] [INFO] Task succeeded: fastANI
[2023-03-17 03:31:15,186] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:31:15,186] [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_900537125.1	s__Shimia sp900537125	86.0934	972	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872815.1	s__Shimia sp014872815	83.5925	876	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	97.10	97.10	0.91	0.91	2	-
GCF_017743735.1	s__Shimia sp017743735	79.7622	630	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_001458175.1	s__Shimia marina	79.5398	556	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_017744095.1	s__Shimia sp017744095	79.3354	564	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	78.9658	463	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	78.7132	472	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143615.1	s__Shimia sp900143615	78.0809	358	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033515.1	s__Ruegeria sp013033515	76.4432	171	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
GCA_018401965.1	s__Roseicyclus sp018401965	76.3776	59	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	76.2301	148	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_900172255.1	s__Roseovarius halotolerans	76.1928	107	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196805.1	s__Sulfitobacter undariae	76.132	114	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:31:15,186] [INFO] GTDB search result was written to OceanDNA-b30154/result_gtdb.tsv
[2023-03-17 03:31:15,186] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:31:15,188] [INFO] DFAST_QC result json was written to OceanDNA-b30154/dqc_result.json
[2023-03-17 03:31:15,188] [INFO] DFAST_QC completed!
[2023-03-17 03:31:15,188] [INFO] Total running time: 0h1m55s