[2023-03-19 04:29:38,146] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,146] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,146] [INFO] DQC Reference Directory: /var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference
[2023-03-19 04:29:39,842] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,842] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,842] [INFO] Running command: cat /var/lib/cwl/stg643069d0-2844-4b3f-9acf-244036259a91/OceanDNA-b30927.fa | prodigal -d OceanDNA-b30927/cds.fna -a OceanDNA-b30927/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:30:04,898] [INFO] Task succeeded: Prodigal
[2023-03-19 04:30:04,899] [INFO] Task started: HMMsearch
[2023-03-19 04:30:04,899] [INFO] Running command: hmmsearch --tblout OceanDNA-b30927/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference/reference_markers.hmm OceanDNA-b30927/protein.faa > /dev/null
[2023-03-19 04:30:05,107] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:30:05,108] [INFO] Found 6/6 markers.
[2023-03-19 04:30:05,131] [INFO] Query marker FASTA was written to OceanDNA-b30927/markers.fasta
[2023-03-19 04:30:05,131] [INFO] Task started: Blastn
[2023-03-19 04:30:05,131] [INFO] Running command: blastn -query OceanDNA-b30927/markers.fasta -db /var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference/reference_markers.fasta -out OceanDNA-b30927/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:05,831] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:05,832] [INFO] Selected 12 target genomes.
[2023-03-19 04:30:05,832] [INFO] Target genome list was writen to OceanDNA-b30927/target_genomes.txt
[2023-03-19 04:30:05,839] [INFO] Task started: fastANI
[2023-03-19 04:30:05,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg643069d0-2844-4b3f-9acf-244036259a91/OceanDNA-b30927.fa --refList OceanDNA-b30927/target_genomes.txt --output OceanDNA-b30927/fastani_result.tsv --threads 1
[2023-03-19 04:30:16,478] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:16,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:16,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:16,484] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2023-03-19 04:30:16,484] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-19 04:30:16,484] [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 tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	96.1657	1262	1301	95	inconclusive
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	96.1548	1256	1301	95	inconclusive
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	95.4676	1186	1301	95	inconclusive
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	94.5854	1215	1301	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	84.5632	972	1301	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	84.104	982	1301	95	below_threshold
Thalassospira lohafexi	strain=139Z-12	GCA_002844275.1	744227	744227	type	True	81.7802	914	1301	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:16,484] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30927/tc_result.tsv
[2023-03-19 04:30:16,484] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:16,485] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:16,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference/checkm_data
[2023-03-19 04:30:16,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:16,686] [INFO] Task started: CheckM
[2023-03-19 04:30:16,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30927/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30927/checkm_input OceanDNA-b30927/checkm_result
[2023-03-19 04:31:18,883] [INFO] Task succeeded: CheckM
[2023-03-19 04:31:18,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:31:18,886] [INFO] ===== Completeness check finished =====
[2023-03-19 04:31:18,886] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:31:18,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30927/markers.fasta)
[2023-03-19 04:31:18,886] [INFO] Task started: Blastn
[2023-03-19 04:31:18,886] [INFO] Running command: blastn -query OceanDNA-b30927/markers.fasta -db /var/lib/cwl/stgebd2743e-bb67-42b9-87ac-8619ebe0dddc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30927/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:31:20,134] [INFO] Task succeeded: Blastn
[2023-03-19 04:31:20,135] [INFO] Selected 8 target genomes.
[2023-03-19 04:31:20,135] [INFO] Target genome list was writen to OceanDNA-b30927/target_genomes_gtdb.txt
[2023-03-19 04:31:20,141] [INFO] Task started: fastANI
[2023-03-19 04:31:20,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg643069d0-2844-4b3f-9acf-244036259a91/OceanDNA-b30927.fa --refList OceanDNA-b30927/target_genomes_gtdb.txt --output OceanDNA-b30927/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:28,079] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:28,084] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:31:28,085] [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_001662875.1	s__Thalassospira tepidiphila	96.1548	1256	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	conclusive
GCF_000300275.1	s__Thalassospira profundimaris	95.4676	1186	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_017922435.1	s__Thalassospira sp017922435	95.1617	1224	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	94.5854	1215	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001613795.1	s__Thalassospira sp001613795	88.2769	1077	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.77	97.25	0.94	0.91	10	-
GCF_000948415.1	s__Thalassospira sp000948415	88.0294	1106	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709775.1	s__Thalassospira sp002709775	87.9644	1019	1301	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	87.5553	1097	1301	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:28,085] [INFO] GTDB search result was written to OceanDNA-b30927/result_gtdb.tsv
[2023-03-19 04:31:28,085] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:28,086] [INFO] DFAST_QC result json was written to OceanDNA-b30927/dqc_result.json
[2023-03-19 04:31:28,086] [INFO] DFAST_QC completed!
[2023-03-19 04:31:28,086] [INFO] Total running time: 0h1m50s