[2023-03-18 02:48:49,291] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:49,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:49,291] [INFO] DQC Reference Directory: /var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference
[2023-03-18 02:48:50,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:50,487] [INFO] Task started: Prodigal
[2023-03-18 02:48:50,487] [INFO] Running command: cat /var/lib/cwl/stg0dc26c60-1212-4674-8bc1-216bd9b56f97/OceanDNA-b30854.fa | prodigal -d OceanDNA-b30854/cds.fna -a OceanDNA-b30854/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:49:14,294] [INFO] Task succeeded: Prodigal
[2023-03-18 02:49:14,294] [INFO] Task started: HMMsearch
[2023-03-18 02:49:14,294] [INFO] Running command: hmmsearch --tblout OceanDNA-b30854/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference/reference_markers.hmm OceanDNA-b30854/protein.faa > /dev/null
[2023-03-18 02:49:14,601] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:49:14,602] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0dc26c60-1212-4674-8bc1-216bd9b56f97/OceanDNA-b30854.fa]
[2023-03-18 02:49:14,626] [INFO] Query marker FASTA was written to OceanDNA-b30854/markers.fasta
[2023-03-18 02:49:14,628] [INFO] Task started: Blastn
[2023-03-18 02:49:14,628] [INFO] Running command: blastn -query OceanDNA-b30854/markers.fasta -db /var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference/reference_markers.fasta -out OceanDNA-b30854/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:15,277] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:15,278] [INFO] Selected 16 target genomes.
[2023-03-18 02:49:15,278] [INFO] Target genome list was writen to OceanDNA-b30854/target_genomes.txt
[2023-03-18 02:49:15,290] [INFO] Task started: fastANI
[2023-03-18 02:49:15,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc26c60-1212-4674-8bc1-216bd9b56f97/OceanDNA-b30854.fa --refList OceanDNA-b30854/target_genomes.txt --output OceanDNA-b30854/fastani_result.tsv --threads 1
[2023-03-18 02:49:27,655] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:27,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:27,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:27,663] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:27,664] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:49:27,664] [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
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	83.1876	929	1229	95	below_threshold
Thalassospira lucentensis	strain=MCCC 1A00383	GCA_003326595.1	168935	168935	type	True	82.8586	921	1229	95	below_threshold
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	82.8477	933	1229	95	below_threshold
Thalassospira lohafexi	strain=139Z-12	GCA_002844275.1	744227	744227	type	True	82.8272	949	1229	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	82.4984	883	1229	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	82.4592	881	1229	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	82.4345	872	1229	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	82.4342	867	1229	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	82.3921	898	1229	95	below_threshold
Thalassospira permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	80.4068	731	1229	95	below_threshold
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	80.3279	731	1229	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:49:27,664] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30854/tc_result.tsv
[2023-03-18 02:49:27,664] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:27,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:27,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference/checkm_data
[2023-03-18 02:49:27,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:27,670] [INFO] Task started: CheckM
[2023-03-18 02:49:27,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30854/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30854/checkm_input OceanDNA-b30854/checkm_result
[2023-03-18 02:50:28,314] [INFO] Task succeeded: CheckM
[2023-03-18 02:50:28,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:50:28,317] [INFO] ===== Completeness check finished =====
[2023-03-18 02:50:28,317] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:50:28,318] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30854/markers.fasta)
[2023-03-18 02:50:28,319] [INFO] Task started: Blastn
[2023-03-18 02:50:28,319] [INFO] Running command: blastn -query OceanDNA-b30854/markers.fasta -db /var/lib/cwl/stge4c1876c-312e-409e-bdbc-85827147b015/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30854/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:50:29,208] [INFO] Task succeeded: Blastn
[2023-03-18 02:50:29,208] [INFO] Selected 15 target genomes.
[2023-03-18 02:50:29,209] [INFO] Target genome list was writen to OceanDNA-b30854/target_genomes_gtdb.txt
[2023-03-18 02:50:29,314] [INFO] Task started: fastANI
[2023-03-18 02:50:29,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg0dc26c60-1212-4674-8bc1-216bd9b56f97/OceanDNA-b30854.fa --refList OceanDNA-b30854/target_genomes_gtdb.txt --output OceanDNA-b30854/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:50:42,972] [INFO] Task succeeded: fastANI
[2023-03-18 02:50:42,980] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:50:42,981] [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_002844235.1	s__Thalassospira povalilytica	83.1809	930	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
GCF_003326795.1	s__Thalassospira profundimaris_C	83.1105	934	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326675.1	s__Thalassospira profundimaris_D	83.0859	929	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421265.1	s__Thalassospira lucentensis	82.8357	935	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	97.14	96.17	0.92	0.88	5	-
GCF_002844275.1	s__Thalassospira lohafexi	82.8334	948	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	82.4654	880	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_017922435.1	s__Thalassospira sp017922435	82.4595	880	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_000763295.1	s__Thalassospira australica	82.4406	866	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300275.1	s__Thalassospira profundimaris	82.4373	872	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	82.3921	898	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002709775.1	s__Thalassospira sp002709775	82.2801	806	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948415.1	s__Thalassospira sp000948415	82.2792	868	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806525.1	s__Thalassospira sp011806525	82.1311	855	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806425.1	s__Thalassospira lucentensis_B	81.8402	824	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115825.1	s__Thalassospira sp002115825	78.0115	407	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:50:42,981] [INFO] GTDB search result was written to OceanDNA-b30854/result_gtdb.tsv
[2023-03-18 02:50:42,981] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:50:42,982] [INFO] DFAST_QC result json was written to OceanDNA-b30854/dqc_result.json
[2023-03-18 02:50:42,983] [INFO] DFAST_QC completed!
[2023-03-18 02:50:42,983] [INFO] Total running time: 0h1m54s