[2023-03-15 10:09:49,681] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:09:49,681] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:09:49,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference
[2023-03-15 10:09:51,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:09:51,537] [INFO] Task started: Prodigal
[2023-03-15 10:09:51,537] [INFO] Running command: cat /var/lib/cwl/stg6aea70b4-295b-47cd-be5e-6c940b32b5b0/OceanDNA-b31643.fa | prodigal -d OceanDNA-b31643/cds.fna -a OceanDNA-b31643/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:10:10,142] [INFO] Task succeeded: Prodigal
[2023-03-15 10:10:10,142] [INFO] Task started: HMMsearch
[2023-03-15 10:10:10,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b31643/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference/reference_markers.hmm OceanDNA-b31643/protein.faa > /dev/null
[2023-03-15 10:10:10,340] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:10:10,341] [INFO] Found 6/6 markers.
[2023-03-15 10:10:10,359] [INFO] Query marker FASTA was written to OceanDNA-b31643/markers.fasta
[2023-03-15 10:10:10,360] [INFO] Task started: Blastn
[2023-03-15 10:10:10,360] [INFO] Running command: blastn -query OceanDNA-b31643/markers.fasta -db /var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference/reference_markers.fasta -out OceanDNA-b31643/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:10:11,077] [INFO] Task succeeded: Blastn
[2023-03-15 10:10:11,078] [INFO] Selected 15 target genomes.
[2023-03-15 10:10:11,078] [INFO] Target genome list was writen to OceanDNA-b31643/target_genomes.txt
[2023-03-15 10:10:11,087] [INFO] Task started: fastANI
[2023-03-15 10:10:11,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg6aea70b4-295b-47cd-be5e-6c940b32b5b0/OceanDNA-b31643.fa --refList OceanDNA-b31643/target_genomes.txt --output OceanDNA-b31643/fastani_result.tsv --threads 1
[2023-03-15 10:10:20,487] [INFO] Task succeeded: fastANI
[2023-03-15 10:10:20,488] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:10:20,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:10:20,497] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:10:20,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:10:20,497] [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
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	85.8413	725	980	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	84.0528	749	980	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	84.026	749	980	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.8289	463	980	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.7143	436	980	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.6087	464	980	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.5178	392	980	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.4713	422	980	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.4172	407	980	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.4009	432	980	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.1477	434	980	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.0645	376	980	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	79.0363	352	980	95	below_threshold
Qipengyuania aerophila	strain=GH25	GCA_019711555.1	2867242	2867242	type	True	78.3203	321	980	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.2383	296	980	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:10:20,497] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31643/tc_result.tsv
[2023-03-15 10:10:20,498] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:10:20,498] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:10:20,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference/checkm_data
[2023-03-15 10:10:20,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:10:20,519] [INFO] Task started: CheckM
[2023-03-15 10:10:20,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31643/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31643/checkm_input OceanDNA-b31643/checkm_result
[2023-03-15 10:11:07,176] [INFO] Task succeeded: CheckM
[2023-03-15 10:11:07,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:11:07,233] [INFO] ===== Completeness check finished =====
[2023-03-15 10:11:07,234] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:11:07,234] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31643/markers.fasta)
[2023-03-15 10:11:07,235] [INFO] Task started: Blastn
[2023-03-15 10:11:07,235] [INFO] Running command: blastn -query OceanDNA-b31643/markers.fasta -db /var/lib/cwl/stg6f1faa95-768d-466e-a4cc-c80d5f4ef189/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31643/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:11:08,408] [INFO] Task succeeded: Blastn
[2023-03-15 10:11:08,411] [INFO] Selected 8 target genomes.
[2023-03-15 10:11:08,411] [INFO] Target genome list was writen to OceanDNA-b31643/target_genomes_gtdb.txt
[2023-03-15 10:11:08,643] [INFO] Task started: fastANI
[2023-03-15 10:11:08,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg6aea70b4-295b-47cd-be5e-6c940b32b5b0/OceanDNA-b31643.fa --refList OceanDNA-b31643/target_genomes_gtdb.txt --output OceanDNA-b31643/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:11:14,066] [INFO] Task succeeded: fastANI
[2023-03-15 10:11:14,072] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 10:11:14,072] [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_002729695.1	s__Alteriqipengyuania sp002729695	98.0089	888	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	conclusive
GCF_015999305.1	s__Alteriqipengyuania sp015999305	85.7728	741	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	85.564	721	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	84.3676	714	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	84.0528	749	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	83.929	682	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	83.8538	365	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	83.8006	682	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:11:14,075] [INFO] GTDB search result was written to OceanDNA-b31643/result_gtdb.tsv
[2023-03-15 10:11:14,076] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:11:14,079] [INFO] DFAST_QC result json was written to OceanDNA-b31643/dqc_result.json
[2023-03-15 10:11:14,079] [INFO] DFAST_QC completed!
[2023-03-15 10:11:14,079] [INFO] Total running time: 0h1m24s