[2023-03-14 11:14:12,736] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,737] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,737] [INFO] DQC Reference Directory: /var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference
[2023-03-14 11:14:14,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,202] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,203] [INFO] Running command: cat /var/lib/cwl/stg35c1acde-6017-479d-85c4-9b4d28397007/OceanDNA-b35244.fa | prodigal -d OceanDNA-b35244/cds.fna -a OceanDNA-b35244/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:31,395] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:31,396] [INFO] Task started: HMMsearch
[2023-03-14 11:14:31,396] [INFO] Running command: hmmsearch --tblout OceanDNA-b35244/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference/reference_markers.hmm OceanDNA-b35244/protein.faa > /dev/null
[2023-03-14 11:14:31,688] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:31,688] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg35c1acde-6017-479d-85c4-9b4d28397007/OceanDNA-b35244.fa]
[2023-03-14 11:14:31,710] [INFO] Query marker FASTA was written to OceanDNA-b35244/markers.fasta
[2023-03-14 11:14:31,715] [INFO] Task started: Blastn
[2023-03-14 11:14:31,716] [INFO] Running command: blastn -query OceanDNA-b35244/markers.fasta -db /var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference/reference_markers.fasta -out OceanDNA-b35244/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:32,409] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:32,410] [INFO] Selected 21 target genomes.
[2023-03-14 11:14:32,410] [INFO] Target genome list was writen to OceanDNA-b35244/target_genomes.txt
[2023-03-14 11:14:32,433] [INFO] Task started: fastANI
[2023-03-14 11:14:32,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c1acde-6017-479d-85c4-9b4d28397007/OceanDNA-b35244.fa --refList OceanDNA-b35244/target_genomes.txt --output OceanDNA-b35244/fastani_result.tsv --threads 1
[2023-03-14 11:14:47,683] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:47,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:47,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:47,695] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:47,695] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:47,696] [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 baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	78.9826	350	1024	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	78.8254	336	1024	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	78.7494	317	1024	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	78.5311	288	1024	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	78.4264	266	1024	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	78.3834	250	1024	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	78.1701	296	1024	95	below_threshold
Shewanella putrefaciens	strain=JCM 20190	GCA_014647555.1	24	24	type	True	78.1374	300	1024	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	78.1371	296	1024	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	78.0488	319	1024	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	77.6715	315	1024	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	77.2251	173	1024	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	77.2126	172	1024	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	77.2123	179	1024	95	below_threshold
Parashewanella curva	strain=C51	GCA_003675895.1	2338552	2338552	type	True	76.841	54	1024	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	76.7797	126	1024	95	below_threshold
Shewanella piezotolerans	strain=WP3	GCA_000014885.1	404011	404011	type	True	76.7742	121	1024	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	76.4358	143	1024	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	76.199	121	1024	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:47,696] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35244/tc_result.tsv
[2023-03-14 11:14:47,696] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:47,696] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:47,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference/checkm_data
[2023-03-14 11:14:47,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:47,750] [INFO] Task started: CheckM
[2023-03-14 11:14:47,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35244/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35244/checkm_input OceanDNA-b35244/checkm_result
[2023-03-14 11:15:33,248] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:33,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:33,251] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:33,251] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:33,251] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35244/markers.fasta)
[2023-03-14 11:15:33,253] [INFO] Task started: Blastn
[2023-03-14 11:15:33,253] [INFO] Running command: blastn -query OceanDNA-b35244/markers.fasta -db /var/lib/cwl/stg28340725-3136-4e97-91e6-c6c4e63d0fe0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35244/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:34,246] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:34,247] [INFO] Selected 21 target genomes.
[2023-03-14 11:15:34,247] [INFO] Target genome list was writen to OceanDNA-b35244/target_genomes_gtdb.txt
[2023-03-14 11:15:34,270] [INFO] Task started: fastANI
[2023-03-14 11:15:34,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c1acde-6017-479d-85c4-9b4d28397007/OceanDNA-b35244.fa --refList OceanDNA-b35244/target_genomes_gtdb.txt --output OceanDNA-b35244/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:49,806] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:49,818] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:49,818] [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_900456975.1	s__Shewanella baltica	78.9898	350	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_002838165.1	s__Shewanella sp002838165	78.8447	343	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_002966515.1	s__Shewanella sp002966515	78.7104	316	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCA_002783505.1	s__Shewanella sp002783505	78.6884	309	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406305.1	s__Shewanella putrefaciens_C	78.5919	311	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406325.1	s__Shewanella putrefaciens	78.1701	296	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_000203935.1	s__Shewanella sp000203935	78.0965	320	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_000485795.1	s__Shewanella decolorationis	78.0533	314	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_002216875.1	s__Shewanella bicestrii	78.0298	331	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.51	96.32	0.89	0.87	4	-
GCF_014647135.1	s__Shewanella xiamenensis	78.0155	300	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.56	97.34	0.92	0.88	25	-
GCF_014648035.1	s__Shewanella algicola	77.2123	179	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	77.1961	173	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_011765625.1	s__Shewanella aestuarii_A	77.1108	139	1024	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	77.0954	162	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_009663145.1	s__Shewanella sp009663145	76.9163	131	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675895.1	s__Parashewanella curva	76.8741	55	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873615.1	s__Shewanella sp002873615	76.8045	148	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605125.1	s__Shewanella algidipiscicola	76.7769	153	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_000014885.1	s__Shewanella piezotolerans	76.7742	121	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019209865.1	s__Shewanella sp019209865	76.6932	112	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765635.1	s__Shewanella schlegeliana	76.4236	144	1024	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:49,819] [INFO] GTDB search result was written to OceanDNA-b35244/result_gtdb.tsv
[2023-03-14 11:15:49,819] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:49,821] [INFO] DFAST_QC result json was written to OceanDNA-b35244/dqc_result.json
[2023-03-14 11:15:49,821] [INFO] DFAST_QC completed!
[2023-03-14 11:15:49,821] [INFO] Total running time: 0h1m37s