[2023-03-18 00:28:55,444] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:28:55,445] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:28:55,445] [INFO] DQC Reference Directory: /var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference
[2023-03-18 00:28:56,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:28:56,559] [INFO] Task started: Prodigal
[2023-03-18 00:28:56,559] [INFO] Running command: cat /var/lib/cwl/stgb58fcf53-9e49-4f87-ad45-35051a8c6cfb/OceanDNA-b30874.fa | prodigal -d OceanDNA-b30874/cds.fna -a OceanDNA-b30874/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:29:27,442] [INFO] Task succeeded: Prodigal
[2023-03-18 00:29:27,443] [INFO] Task started: HMMsearch
[2023-03-18 00:29:27,443] [INFO] Running command: hmmsearch --tblout OceanDNA-b30874/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference/reference_markers.hmm OceanDNA-b30874/protein.faa > /dev/null
[2023-03-18 00:29:27,667] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:29:27,668] [INFO] Found 6/6 markers.
[2023-03-18 00:29:27,694] [INFO] Query marker FASTA was written to OceanDNA-b30874/markers.fasta
[2023-03-18 00:29:27,695] [INFO] Task started: Blastn
[2023-03-18 00:29:27,695] [INFO] Running command: blastn -query OceanDNA-b30874/markers.fasta -db /var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference/reference_markers.fasta -out OceanDNA-b30874/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:29:28,368] [INFO] Task succeeded: Blastn
[2023-03-18 00:29:28,369] [INFO] Selected 14 target genomes.
[2023-03-18 00:29:28,369] [INFO] Target genome list was writen to OceanDNA-b30874/target_genomes.txt
[2023-03-18 00:29:28,377] [INFO] Task started: fastANI
[2023-03-18 00:29:28,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgb58fcf53-9e49-4f87-ad45-35051a8c6cfb/OceanDNA-b30874.fa --refList OceanDNA-b30874/target_genomes.txt --output OceanDNA-b30874/fastani_result.tsv --threads 1
[2023-03-18 00:29:39,967] [INFO] Task succeeded: fastANI
[2023-03-18 00:29:39,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:29:39,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:29:39,974] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2023-03-18 00:29:39,975] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-18 00:29:39,975] [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 lucentensis	strain=MCCC 1A00383	GCA_003326595.1	168935	168935	type	True	96.2902	1386	1561	95	inconclusive
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	96.261	1393	1561	95	inconclusive
Thalassospira lohafexi	strain=139Z-12	GCA_002844275.1	744227	744227	type	True	95.8693	1392	1561	95	inconclusive
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	82.2921	1046	1561	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	81.9795	1002	1561	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	81.9492	1003	1561	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	81.9168	990	1561	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	81.9038	1013	1561	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	81.8389	984	1561	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:29:39,975] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30874/tc_result.tsv
[2023-03-18 00:29:39,975] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:29:39,975] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:29:39,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference/checkm_data
[2023-03-18 00:29:39,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:29:39,981] [INFO] Task started: CheckM
[2023-03-18 00:29:39,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30874/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30874/checkm_input OceanDNA-b30874/checkm_result
[2023-03-18 00:30:57,824] [INFO] Task succeeded: CheckM
[2023-03-18 00:30:57,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:30:57,827] [INFO] ===== Completeness check finished =====
[2023-03-18 00:30:57,828] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:30:57,828] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30874/markers.fasta)
[2023-03-18 00:30:57,829] [INFO] Task started: Blastn
[2023-03-18 00:30:57,829] [INFO] Running command: blastn -query OceanDNA-b30874/markers.fasta -db /var/lib/cwl/stgef705b37-7f77-4cf6-8a78-af80bf66537d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30874/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:30:59,358] [INFO] Task succeeded: Blastn
[2023-03-18 00:30:59,359] [INFO] Selected 11 target genomes.
[2023-03-18 00:30:59,359] [INFO] Target genome list was writen to OceanDNA-b30874/target_genomes_gtdb.txt
[2023-03-18 00:30:59,372] [INFO] Task started: fastANI
[2023-03-18 00:30:59,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgb58fcf53-9e49-4f87-ad45-35051a8c6cfb/OceanDNA-b30874.fa --refList OceanDNA-b30874/target_genomes_gtdb.txt --output OceanDNA-b30874/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:31:10,382] [INFO] Task succeeded: fastANI
[2023-03-18 00:31:10,389] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:31:10,389] [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_000421265.1	s__Thalassospira lucentensis	96.261	1393	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	97.14	96.17	0.92	0.88	5	conclusive
GCF_002844275.1	s__Thalassospira lohafexi	95.8693	1392	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_011806425.1	s__Thalassospira lucentensis_B	84.2842	1105	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844235.1	s__Thalassospira povalilytica	82.2921	1046	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
GCF_003326675.1	s__Thalassospira profundimaris_D	82.0079	1041	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	81.9567	1002	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000300275.1	s__Thalassospira profundimaris	81.9109	991	1561	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	81.8991	1014	1561	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	81.8952	1008	1561	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	81.8296	986	1561	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	81.7105	964	1561	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 00:31:10,389] [INFO] GTDB search result was written to OceanDNA-b30874/result_gtdb.tsv
[2023-03-18 00:31:10,390] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:31:10,392] [INFO] DFAST_QC result json was written to OceanDNA-b30874/dqc_result.json
[2023-03-18 00:31:10,392] [INFO] DFAST_QC completed!
[2023-03-18 00:31:10,392] [INFO] Total running time: 0h2m15s