[2023-03-17 06:30:51,134] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:51,134] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:51,135] [INFO] DQC Reference Directory: /var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference
[2023-03-17 06:30:52,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:52,270] [INFO] Task started: Prodigal
[2023-03-17 06:30:52,270] [INFO] Running command: cat /var/lib/cwl/stgbd81d36e-7a5a-46ef-a9a7-8e6dc4183953/OceanDNA-b35246.fa | prodigal -d OceanDNA-b35246/cds.fna -a OceanDNA-b35246/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:14,210] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:14,210] [INFO] Task started: HMMsearch
[2023-03-17 06:31:14,210] [INFO] Running command: hmmsearch --tblout OceanDNA-b35246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference/reference_markers.hmm OceanDNA-b35246/protein.faa > /dev/null
[2023-03-17 06:31:14,455] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:14,456] [INFO] Found 6/6 markers.
[2023-03-17 06:31:14,479] [INFO] Query marker FASTA was written to OceanDNA-b35246/markers.fasta
[2023-03-17 06:31:14,480] [INFO] Task started: Blastn
[2023-03-17 06:31:14,480] [INFO] Running command: blastn -query OceanDNA-b35246/markers.fasta -db /var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference/reference_markers.fasta -out OceanDNA-b35246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:15,196] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:15,196] [INFO] Selected 16 target genomes.
[2023-03-17 06:31:15,197] [INFO] Target genome list was writen to OceanDNA-b35246/target_genomes.txt
[2023-03-17 06:31:15,205] [INFO] Task started: fastANI
[2023-03-17 06:31:15,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd81d36e-7a5a-46ef-a9a7-8e6dc4183953/OceanDNA-b35246.fa --refList OceanDNA-b35246/target_genomes.txt --output OceanDNA-b35246/fastani_result.tsv --threads 1
[2023-03-17 06:31:28,729] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:28,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:28,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:28,739] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 06:31:28,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 06:31:28,739] [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
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	95.4376	1177	1349	95	conclusive
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	82.1158	831	1349	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	82.0982	840	1349	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	79.8227	485	1349	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	79.814	475	1349	95	below_threshold
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	79.6611	524	1349	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	79.6575	473	1349	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	79.3836	493	1349	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	79.3433	476	1349	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	79.3012	490	1349	95	below_threshold
Shewanella polaris	strain=SM1901	GCA_006385555.1	2588449	2588449	type	True	79.2931	475	1349	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	79.2476	480	1349	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	79.2386	482	1349	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	78.9684	485	1349	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	78.4592	352	1349	95	below_threshold
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	78.1027	330	1349	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:28,740] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35246/tc_result.tsv
[2023-03-17 06:31:28,740] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:28,740] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:28,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference/checkm_data
[2023-03-17 06:31:28,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:28,746] [INFO] Task started: CheckM
[2023-03-17 06:31:28,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35246/checkm_input OceanDNA-b35246/checkm_result
[2023-03-17 06:32:23,621] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:23,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:23,624] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:23,624] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:23,624] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35246/markers.fasta)
[2023-03-17 06:32:23,624] [INFO] Task started: Blastn
[2023-03-17 06:32:23,624] [INFO] Running command: blastn -query OceanDNA-b35246/markers.fasta -db /var/lib/cwl/stg167a91b8-1f27-4d67-9b1c-b22294d5783a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:24,654] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:24,655] [INFO] Selected 16 target genomes.
[2023-03-17 06:32:24,655] [INFO] Target genome list was writen to OceanDNA-b35246/target_genomes_gtdb.txt
[2023-03-17 06:32:24,757] [INFO] Task started: fastANI
[2023-03-17 06:32:24,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd81d36e-7a5a-46ef-a9a7-8e6dc4183953/OceanDNA-b35246.fa --refList OceanDNA-b35246/target_genomes_gtdb.txt --output OceanDNA-b35246/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:38,248] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:38,257] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:38,257] [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_014647215.1	s__Shewanella aestuarii	82.1249	830	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	79.8221	485	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_010092445.1	s__Shewanella sp002836315	79.679	502	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_003855395.1	s__Shewanella livingstonensis	79.6659	524	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014164505.1	s__Shewanella sp014164505	79.6594	406	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648315.1	s__Shewanella ulleungensis	79.6077	474	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011765625.1	s__Shewanella aestuarii_A	79.6052	584	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	79.5896	512	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014648035.1	s__Shewanella algicola	79.4695	467	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	79.3836	493	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014641855.1	s__Shewanella inventionis	79.311	489	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	79.2929	475	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_014648295.1	s__Shewanella saliphila	79.2677	478	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_009663145.1	s__Shewanella sp009663145	78.5281	312	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013765.1	s__Shewanella denitrificans	78.4631	287	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.1056	329	1349	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:38,258] [INFO] GTDB search result was written to OceanDNA-b35246/result_gtdb.tsv
[2023-03-17 06:32:38,258] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:38,259] [INFO] DFAST_QC result json was written to OceanDNA-b35246/dqc_result.json
[2023-03-17 06:32:38,260] [INFO] DFAST_QC completed!
[2023-03-17 06:32:38,260] [INFO] Total running time: 0h1m47s