[2023-03-17 11:57:19,291] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference
[2023-03-17 11:57:20,886] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,887] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,887] [INFO] Running command: cat /var/lib/cwl/stgb257d442-e11a-4c52-ae6b-f25b97186977/OceanDNA-b7262.fa | prodigal -d OceanDNA-b7262/cds.fna -a OceanDNA-b7262/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:32,589] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:32,589] [INFO] Task started: HMMsearch
[2023-03-17 11:57:32,590] [INFO] Running command: hmmsearch --tblout OceanDNA-b7262/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference/reference_markers.hmm OceanDNA-b7262/protein.faa > /dev/null
[2023-03-17 11:57:32,759] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:32,760] [INFO] Found 6/6 markers.
[2023-03-17 11:57:32,772] [INFO] Query marker FASTA was written to OceanDNA-b7262/markers.fasta
[2023-03-17 11:57:32,772] [INFO] Task started: Blastn
[2023-03-17 11:57:32,772] [INFO] Running command: blastn -query OceanDNA-b7262/markers.fasta -db /var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference/reference_markers.fasta -out OceanDNA-b7262/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:33,367] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:33,367] [INFO] Selected 29 target genomes.
[2023-03-17 11:57:33,368] [INFO] Target genome list was writen to OceanDNA-b7262/target_genomes.txt
[2023-03-17 11:57:33,382] [INFO] Task started: fastANI
[2023-03-17 11:57:33,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgb257d442-e11a-4c52-ae6b-f25b97186977/OceanDNA-b7262.fa --refList OceanDNA-b7262/target_genomes.txt --output OceanDNA-b7262/fastani_result.tsv --threads 1
[2023-03-17 11:57:48,957] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:48,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:48,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:48,969] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:48,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:57:48,970] [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
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	77.128	159	589	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.9869	158	589	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.39	66	589	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	76.2757	55	589	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.0813	72	589	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.071	56	589	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.0431	65	589	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.0138	78	589	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	76.0071	69	589	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	75.9865	51	589	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	75.95	57	589	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	75.8996	61	589	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	75.893	56	589	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.8588	50	589	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	75.7517	52	589	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.7457	56	589	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	75.5794	60	589	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	75.4715	64	589	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	75.4653	67	589	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	75.3013	64	589	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	75.227	63	589	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:57:48,970] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7262/tc_result.tsv
[2023-03-17 11:57:48,970] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:48,970] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:48,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference/checkm_data
[2023-03-17 11:57:48,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:48,974] [INFO] Task started: CheckM
[2023-03-17 11:57:48,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7262/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7262/checkm_input OceanDNA-b7262/checkm_result
[2023-03-17 11:58:21,778] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:21,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:21,780] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:21,781] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:21,781] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7262/markers.fasta)
[2023-03-17 11:58:21,781] [INFO] Task started: Blastn
[2023-03-17 11:58:21,781] [INFO] Running command: blastn -query OceanDNA-b7262/markers.fasta -db /var/lib/cwl/stgcfb808cf-e921-4939-99b5-5ee341a9e1e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7262/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:22,634] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:22,634] [INFO] Selected 18 target genomes.
[2023-03-17 11:58:22,635] [INFO] Target genome list was writen to OceanDNA-b7262/target_genomes_gtdb.txt
[2023-03-17 11:58:22,806] [INFO] Task started: fastANI
[2023-03-17 11:58:22,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgb257d442-e11a-4c52-ae6b-f25b97186977/OceanDNA-b7262.fa --refList OceanDNA-b7262/target_genomes_gtdb.txt --output OceanDNA-b7262/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:31,565] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:31,574] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:58:31,575] [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_003450155.1	s__Patiriisocius sp003450155	81.9749	377	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182755.1	s__Patiriisocius sp905182755	81.8343	385	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	96.66	96.28	0.84	0.84	6	-
GCA_018656255.1	s__Patiriisocius sp018656255	81.0537	304	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	97.76	97.76	0.76	0.76	2	-
GCF_008974325.1	s__Patiriisocius marinus	77.1304	158	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009014635.1	s__Patiriisocius marinistellae	76.9734	159	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000170815.1	s__Patiriisocius sp000170815	76.8084	128	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.3417	71	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011044175.1	s__Marinirhabdus sp011044175	76.2746	91	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.2723	53	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.144	77	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.0491	57	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.0236	82	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	75.9912	67	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	75.8291	54	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	75.7032	66	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:31,575] [INFO] GTDB search result was written to OceanDNA-b7262/result_gtdb.tsv
[2023-03-17 11:58:31,575] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:31,577] [INFO] DFAST_QC result json was written to OceanDNA-b7262/dqc_result.json
[2023-03-17 11:58:31,577] [INFO] DFAST_QC completed!
[2023-03-17 11:58:31,577] [INFO] Total running time: 0h1m12s