[2023-03-15 14:06:11,285] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,285] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference
[2023-03-15 14:06:12,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,387] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,388] [INFO] Running command: cat /var/lib/cwl/stg62e7b56b-e13d-40a9-aa9d-da2ea9dd8427/OceanDNA-b7003.fa | prodigal -d OceanDNA-b7003/cds.fna -a OceanDNA-b7003/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:28,983] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:28,984] [INFO] Task started: HMMsearch
[2023-03-15 14:06:28,984] [INFO] Running command: hmmsearch --tblout OceanDNA-b7003/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference/reference_markers.hmm OceanDNA-b7003/protein.faa > /dev/null
[2023-03-15 14:06:29,200] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:29,200] [INFO] Found 6/6 markers.
[2023-03-15 14:06:29,218] [INFO] Query marker FASTA was written to OceanDNA-b7003/markers.fasta
[2023-03-15 14:06:29,218] [INFO] Task started: Blastn
[2023-03-15 14:06:29,218] [INFO] Running command: blastn -query OceanDNA-b7003/markers.fasta -db /var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference/reference_markers.fasta -out OceanDNA-b7003/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:29,830] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:29,831] [INFO] Selected 34 target genomes.
[2023-03-15 14:06:29,832] [INFO] Target genome list was writen to OceanDNA-b7003/target_genomes.txt
[2023-03-15 14:06:29,853] [INFO] Task started: fastANI
[2023-03-15 14:06:29,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg62e7b56b-e13d-40a9-aa9d-da2ea9dd8427/OceanDNA-b7003.fa --refList OceanDNA-b7003/target_genomes.txt --output OceanDNA-b7003/fastani_result.tsv --threads 1
[2023-03-15 14:06:50,051] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:50,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:50,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:50,069] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:50,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:06:50,070] [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 marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.6635	129	887	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.6134	117	887	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.5399	139	887	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.5368	178	887	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.5308	101	887	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.4821	110	887	95	below_threshold
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	76.4439	137	887	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.3792	94	887	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.3257	124	887	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.2939	72	887	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.2913	109	887	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.2813	141	887	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.2503	149	887	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.2269	77	887	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.1392	92	887	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.0303	115	887	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.0287	105	887	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.0105	107	887	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.005	83	887	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.9887	96	887	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.9872	110	887	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	75.9766	114	887	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	75.973	111	887	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	75.973	111	887	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	75.9615	56	887	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	75.9452	76	887	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	75.8481	106	887	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	75.7911	57	887	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	75.7378	64	887	95	below_threshold
Flavobacterium swingsii	strain=DSM 21789	GCA_900111965.1	498292	498292	type	True	75.6853	66	887	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	75.5917	76	887	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.5601	99	887	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.3727	69	887	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:06:50,070] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7003/tc_result.tsv
[2023-03-15 14:06:50,071] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:50,071] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:50,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference/checkm_data
[2023-03-15 14:06:50,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:50,242] [INFO] Task started: CheckM
[2023-03-15 14:06:50,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7003/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7003/checkm_input OceanDNA-b7003/checkm_result
[2023-03-15 14:07:32,995] [INFO] Task succeeded: CheckM
[2023-03-15 14:07:32,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:07:32,999] [INFO] ===== Completeness check finished =====
[2023-03-15 14:07:32,999] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:07:32,999] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7003/markers.fasta)
[2023-03-15 14:07:33,000] [INFO] Task started: Blastn
[2023-03-15 14:07:33,001] [INFO] Running command: blastn -query OceanDNA-b7003/markers.fasta -db /var/lib/cwl/stg693c62c0-1fa1-4bf9-8df9-42034651893d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7003/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:07:33,838] [INFO] Task succeeded: Blastn
[2023-03-15 14:07:33,840] [INFO] Selected 12 target genomes.
[2023-03-15 14:07:33,840] [INFO] Target genome list was writen to OceanDNA-b7003/target_genomes_gtdb.txt
[2023-03-15 14:07:33,884] [INFO] Task started: fastANI
[2023-03-15 14:07:33,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg62e7b56b-e13d-40a9-aa9d-da2ea9dd8427/OceanDNA-b7003.fa --refList OceanDNA-b7003/target_genomes_gtdb.txt --output OceanDNA-b7003/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:07:39,868] [INFO] Task succeeded: fastANI
[2023-03-15 14:07:39,876] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:07:39,876] [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_018669795.1	s__GCA-002733185 sp018669795	87.4772	562	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCA_002713705.1	s__GCA-002733185 sp002713705	84.7616	549	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_002733185.1	s__GCA-002733185 sp002733185	79.0731	386	887	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_905181835.1	s__GCA-002733185 sp905181835	78.4131	312	887	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_004214175.1	s__GCA-002733185 sp004214175	78.0882	212	887	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_004213605.1	s__GCA-002733185 sp004213605	78.0289	221	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCA_019090365.1	s__GCA-002733185 sp019090365	77.7304	237	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.2893	108	887	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_008086165.1	s__Algorimicrobium algoritergicola	76.2064	125	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002360635.1	s__Marixanthomonas sp002360635	76.1556	123	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.0287	105	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	75.7614	71	887	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-03-15 14:07:39,877] [INFO] GTDB search result was written to OceanDNA-b7003/result_gtdb.tsv
[2023-03-15 14:07:39,878] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:07:39,881] [INFO] DFAST_QC result json was written to OceanDNA-b7003/dqc_result.json
[2023-03-15 14:07:39,881] [INFO] DFAST_QC completed!
[2023-03-15 14:07:39,881] [INFO] Total running time: 0h1m29s