[2023-03-17 03:11:36,377] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,377] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,377] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference
[2023-03-17 03:11:37,513] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,514] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,514] [INFO] Running command: cat /var/lib/cwl/stg6edce8a5-dc7d-49bf-b21d-18cda5b6685f/OceanDNA-b31467.fa | prodigal -d OceanDNA-b31467/cds.fna -a OceanDNA-b31467/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:11:58,721] [INFO] Task succeeded: Prodigal
[2023-03-17 03:11:58,722] [INFO] Task started: HMMsearch
[2023-03-17 03:11:58,722] [INFO] Running command: hmmsearch --tblout OceanDNA-b31467/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference/reference_markers.hmm OceanDNA-b31467/protein.faa > /dev/null
[2023-03-17 03:11:58,990] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:11:58,990] [INFO] Found 6/6 markers.
[2023-03-17 03:11:59,012] [INFO] Query marker FASTA was written to OceanDNA-b31467/markers.fasta
[2023-03-17 03:11:59,012] [INFO] Task started: Blastn
[2023-03-17 03:11:59,012] [INFO] Running command: blastn -query OceanDNA-b31467/markers.fasta -db /var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference/reference_markers.fasta -out OceanDNA-b31467/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:11:59,688] [INFO] Task succeeded: Blastn
[2023-03-17 03:11:59,689] [INFO] Selected 14 target genomes.
[2023-03-17 03:11:59,689] [INFO] Target genome list was writen to OceanDNA-b31467/target_genomes.txt
[2023-03-17 03:11:59,717] [INFO] Task started: fastANI
[2023-03-17 03:11:59,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg6edce8a5-dc7d-49bf-b21d-18cda5b6685f/OceanDNA-b31467.fa --refList OceanDNA-b31467/target_genomes.txt --output OceanDNA-b31467/fastani_result.tsv --threads 1
[2023-03-17 03:12:10,390] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:10,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:12:10,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:12:10,397] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:12:10,397] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:12:10,397] [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
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	80.6233	606	1164	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	80.5875	614	1164	95	below_threshold
Sneathiella sedimenti	strain=CAU 1612	GCA_017313765.1	2816034	2816034	type	True	79.7428	583	1164	95	below_threshold
Sneathiella litorea	strain=DP05	GCA_009882915.1	2606216	2606216	type	True	79.3772	479	1164	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	76.8387	182	1164	95	below_threshold
Sneathiella glossodoripedis	strain=JCM 23214	GCA_000616095.1	418853	418853	type	True	76.1493	52	1164	95	below_threshold
Sneathiella limimaris	strain=KCTC 52846	GCA_012932565.1	1964213	1964213	type	True	76.0132	76	1164	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:12:10,397] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31467/tc_result.tsv
[2023-03-17 03:12:10,397] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:12:10,397] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:12:10,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference/checkm_data
[2023-03-17 03:12:10,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:12:10,434] [INFO] Task started: CheckM
[2023-03-17 03:12:10,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31467/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31467/checkm_input OceanDNA-b31467/checkm_result
[2023-03-17 03:13:03,720] [INFO] Task succeeded: CheckM
[2023-03-17 03:13:03,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:13:03,723] [INFO] ===== Completeness check finished =====
[2023-03-17 03:13:03,723] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:13:03,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31467/markers.fasta)
[2023-03-17 03:13:03,724] [INFO] Task started: Blastn
[2023-03-17 03:13:03,724] [INFO] Running command: blastn -query OceanDNA-b31467/markers.fasta -db /var/lib/cwl/stgb4a3ee62-cd5f-4376-80fd-098d5d908352/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31467/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:13:04,916] [INFO] Task succeeded: Blastn
[2023-03-17 03:13:04,917] [INFO] Selected 8 target genomes.
[2023-03-17 03:13:04,917] [INFO] Target genome list was writen to OceanDNA-b31467/target_genomes_gtdb.txt
[2023-03-17 03:13:05,008] [INFO] Task started: fastANI
[2023-03-17 03:13:05,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg6edce8a5-dc7d-49bf-b21d-18cda5b6685f/OceanDNA-b31467.fa --refList OceanDNA-b31467/target_genomes_gtdb.txt --output OceanDNA-b31467/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:13:10,776] [INFO] Task succeeded: fastANI
[2023-03-17 03:13:10,782] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:13:10,782] [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_002706985.1	s__Sneathiella sp002706985	99.7256	985	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.70	99.70	0.85	0.85	2	conclusive
GCF_009882935.1	s__Sneathiella chungangensis	80.5777	615	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017313765.1	s__Sneathiella sp017313765	79.7428	583	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882915.1	s__Sneathiella litorea	79.3772	479	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694385.1	s__Sneathiella sp002694385	79.307	487	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	95.34	95.31	0.92	0.91	3	-
GCF_000616095.1	s__Sneathiella glossodoripedis	76.1777	51	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932565.1	s__Sneathiella limimaris	76.0349	75	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015143595.1	s__Sneathiella sp015143595	75.9267	67	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:13:10,782] [INFO] GTDB search result was written to OceanDNA-b31467/result_gtdb.tsv
[2023-03-17 03:13:10,782] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:13:10,783] [INFO] DFAST_QC result json was written to OceanDNA-b31467/dqc_result.json
[2023-03-17 03:13:10,784] [INFO] DFAST_QC completed!
[2023-03-17 03:13:10,784] [INFO] Total running time: 0h1m34s