[2023-03-15 10:21:46,238] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,238] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,238] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference
[2023-03-15 10:21:47,933] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,933] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,933] [INFO] Running command: cat /var/lib/cwl/stgdd1dedff-ebf8-459c-a161-65522c0f5bed/OceanDNA-b6748.fa | prodigal -d OceanDNA-b6748/cds.fna -a OceanDNA-b6748/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:22:15,227] [INFO] Task succeeded: Prodigal
[2023-03-15 10:22:15,228] [INFO] Task started: HMMsearch
[2023-03-15 10:22:15,228] [INFO] Running command: hmmsearch --tblout OceanDNA-b6748/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference/reference_markers.hmm OceanDNA-b6748/protein.faa > /dev/null
[2023-03-15 10:22:15,459] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:15,460] [INFO] Found 6/6 markers.
[2023-03-15 10:22:15,485] [INFO] Query marker FASTA was written to OceanDNA-b6748/markers.fasta
[2023-03-15 10:22:15,486] [INFO] Task started: Blastn
[2023-03-15 10:22:15,486] [INFO] Running command: blastn -query OceanDNA-b6748/markers.fasta -db /var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference/reference_markers.fasta -out OceanDNA-b6748/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:16,077] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:16,078] [INFO] Selected 19 target genomes.
[2023-03-15 10:22:16,078] [INFO] Target genome list was writen to OceanDNA-b6748/target_genomes.txt
[2023-03-15 10:22:16,086] [INFO] Task started: fastANI
[2023-03-15 10:22:16,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1dedff-ebf8-459c-a161-65522c0f5bed/OceanDNA-b6748.fa --refList OceanDNA-b6748/target_genomes.txt --output OceanDNA-b6748/fastani_result.tsv --threads 1
[2023-03-15 10:22:29,822] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:29,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:29,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:29,833] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:29,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:29,833] [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
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	80.425	836	1408	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	80.4178	839	1408	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	76.8649	209	1408	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	76.7972	204	1408	95	below_threshold
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	76.6824	191	1408	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.0907	120	1408	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.0552	69	1408	95	below_threshold
Croceibacter atlanticus	strain=HTCC2559	GCA_000196315.1	313588	313588	type	True	76.0448	73	1408	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.9055	83	1408	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	75.9031	91	1408	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.8807	73	1408	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	75.8195	92	1408	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	75.8195	92	1408	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	75.7774	88	1408	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	75.7308	71	1408	95	below_threshold
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	75.7085	108	1408	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.6922	70	1408	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	75.5643	81	1408	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:29,834] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6748/tc_result.tsv
[2023-03-15 10:22:29,834] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:29,834] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:29,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference/checkm_data
[2023-03-15 10:22:29,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:29,840] [INFO] Task started: CheckM
[2023-03-15 10:22:29,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6748/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6748/checkm_input OceanDNA-b6748/checkm_result
[2023-03-15 10:23:36,759] [INFO] Task succeeded: CheckM
[2023-03-15 10:23:36,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:23:36,763] [INFO] ===== Completeness check finished =====
[2023-03-15 10:23:36,763] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:23:36,763] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6748/markers.fasta)
[2023-03-15 10:23:36,764] [INFO] Task started: Blastn
[2023-03-15 10:23:36,765] [INFO] Running command: blastn -query OceanDNA-b6748/markers.fasta -db /var/lib/cwl/stg3cdf3bd0-90b7-45a2-816b-ed1381617ee1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6748/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:23:37,586] [INFO] Task succeeded: Blastn
[2023-03-15 10:23:37,587] [INFO] Selected 23 target genomes.
[2023-03-15 10:23:37,587] [INFO] Target genome list was writen to OceanDNA-b6748/target_genomes_gtdb.txt
[2023-03-15 10:23:38,787] [INFO] Task started: fastANI
[2023-03-15 10:23:38,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1dedff-ebf8-459c-a161-65522c0f5bed/OceanDNA-b6748.fa --refList OceanDNA-b6748/target_genomes_gtdb.txt --output OceanDNA-b6748/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:23:52,755] [INFO] Task succeeded: fastANI
[2023-03-15 10:23:52,768] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:23:52,768] [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_900188275.1	s__Dokdonia pacifica	80.4209	837	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000355805.1	s__Dokdonia sp000355805	77.1287	194	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212355.1	s__Dokdonia sp000212355	77.0701	206	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_007827465.1	s__Dokdonia sp007827465	76.989	155	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095655.1	s__Dokdonia sp003095655	76.8948	218	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	76.8205	201	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCF_003688895.1	s__Dokdonia sinensis	76.6824	190	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712765.1	s__Dokdonia sp002712765	76.5967	127	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	99.61	99.61	0.82	0.82	2	-
GCF_001418105.1	s__Oceanihabitans himadriensis	76.105	119	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.0948	123	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	76.0552	69	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000196315.1	s__Croceibacter atlanticus	76.0448	73	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceibacter	95.0	98.48	98.33	0.94	0.89	6	-
GCF_000826655.1	s__Psychroserpens damuponensis	76.0272	105	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	75.8746	98	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_000934685.1	s__Lacinutrix sp000934685	75.8418	82	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	75.8389	91	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	75.8195	92	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011777505.1	s__CAU-1491 sp011777505	75.7841	87	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735115.1	s__Aquimarina mytili	75.7085	108	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	75.6854	86	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	75.6687	95	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009764685.1	s__Flavobacterium sp009764685	75.1469	60	1408	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:23:52,768] [INFO] GTDB search result was written to OceanDNA-b6748/result_gtdb.tsv
[2023-03-15 10:23:52,768] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:23:52,770] [INFO] DFAST_QC result json was written to OceanDNA-b6748/dqc_result.json
[2023-03-15 10:23:52,770] [INFO] DFAST_QC completed!
[2023-03-15 10:23:52,771] [INFO] Total running time: 0h2m7s