[2023-03-15 21:01:44,368] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,368] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,368] [INFO] DQC Reference Directory: /var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stgf28b1f54-d4d2-4fe4-a4ca-ceacccd0fb8c/OceanDNA-b34666.fa | prodigal -d OceanDNA-b34666/cds.fna -a OceanDNA-b34666/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:07,219] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:07,220] [INFO] Task started: HMMsearch
[2023-03-15 21:02:07,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b34666/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference/reference_markers.hmm OceanDNA-b34666/protein.faa > /dev/null
[2023-03-15 21:02:07,454] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:07,455] [INFO] Found 6/6 markers.
[2023-03-15 21:02:07,477] [INFO] Query marker FASTA was written to OceanDNA-b34666/markers.fasta
[2023-03-15 21:02:07,477] [INFO] Task started: Blastn
[2023-03-15 21:02:07,478] [INFO] Running command: blastn -query OceanDNA-b34666/markers.fasta -db /var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference/reference_markers.fasta -out OceanDNA-b34666/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:08,120] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:08,121] [INFO] Selected 21 target genomes.
[2023-03-15 21:02:08,122] [INFO] Target genome list was writen to OceanDNA-b34666/target_genomes.txt
[2023-03-15 21:02:08,134] [INFO] Task started: fastANI
[2023-03-15 21:02:08,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28b1f54-d4d2-4fe4-a4ca-ceacccd0fb8c/OceanDNA-b34666.fa --refList OceanDNA-b34666/target_genomes.txt --output OceanDNA-b34666/fastani_result.tsv --threads 1
[2023-03-15 21:02:23,117] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:23,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:23,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:23,127] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:23,127] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:23,128] [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
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.6534	456	1364	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.6391	353	1364	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.5608	299	1364	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.473	344	1364	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.4009	325	1364	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.3718	303	1364	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.1677	236	1364	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.1645	313	1364	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.8753	281	1364	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.8675	231	1364	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.5776	212	1364	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.5613	188	1364	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.499	185	1364	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.4808	79	1364	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.1224	70	1364	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	75.9256	60	1364	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	75.8999	61	1364	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:23,128] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34666/tc_result.tsv
[2023-03-15 21:02:23,128] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:23,128] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:23,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference/checkm_data
[2023-03-15 21:02:23,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:23,134] [INFO] Task started: CheckM
[2023-03-15 21:02:23,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34666/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34666/checkm_input OceanDNA-b34666/checkm_result
[2023-03-15 21:03:17,122] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:17,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:17,125] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:17,125] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:17,125] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34666/markers.fasta)
[2023-03-15 21:03:17,126] [INFO] Task started: Blastn
[2023-03-15 21:03:17,126] [INFO] Running command: blastn -query OceanDNA-b34666/markers.fasta -db /var/lib/cwl/stg66431048-e9d7-4b88-ad92-2dd430e16667/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34666/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:18,173] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:18,174] [INFO] Selected 12 target genomes.
[2023-03-15 21:03:18,174] [INFO] Target genome list was writen to OceanDNA-b34666/target_genomes_gtdb.txt
[2023-03-15 21:03:18,434] [INFO] Task started: fastANI
[2023-03-15 21:03:18,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28b1f54-d4d2-4fe4-a4ca-ceacccd0fb8c/OceanDNA-b34666.fa --refList OceanDNA-b34666/target_genomes_gtdb.txt --output OceanDNA-b34666/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:28,605] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:28,613] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:28,613] [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_003333305.1	s__Colwellia aromaticivorans	85.0263	851	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215465.1	s__Colwellia sp013215465	83.6002	864	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCA_002733765.1	s__Colwellia sp002733765	83.48	814	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_003521815.1	s__Colwellia sp003521815	83.3181	582	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	79.7474	407	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	79.7026	468	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_007954275.1	s__Colwellia demingiae	79.673	455	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016745015.1	s__Colwellia sp016745015	79.6105	464	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832865.1	s__Colwellia sp009832865	79.2077	463	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	78.7914	364	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCA_016765685.1	s__Colwellia sp016765685	78.5707	323	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.5599	305	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:28,613] [INFO] GTDB search result was written to OceanDNA-b34666/result_gtdb.tsv
[2023-03-15 21:03:28,613] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:28,615] [INFO] DFAST_QC result json was written to OceanDNA-b34666/dqc_result.json
[2023-03-15 21:03:28,615] [INFO] DFAST_QC completed!
[2023-03-15 21:03:28,615] [INFO] Total running time: 0h1m44s