[2023-03-15 16:25:57,006] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,010] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference
[2023-03-15 16:25:58,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,595] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,595] [INFO] Running command: cat /var/lib/cwl/stga49139ac-57b3-48e8-bfba-99fb9a475a08/OceanDNA-b31616.fa | prodigal -d OceanDNA-b31616/cds.fna -a OceanDNA-b31616/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:16,261] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:16,262] [INFO] Task started: HMMsearch
[2023-03-15 16:26:16,262] [INFO] Running command: hmmsearch --tblout OceanDNA-b31616/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference/reference_markers.hmm OceanDNA-b31616/protein.faa > /dev/null
[2023-03-15 16:26:16,446] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:16,447] [INFO] Found 6/6 markers.
[2023-03-15 16:26:16,523] [INFO] Query marker FASTA was written to OceanDNA-b31616/markers.fasta
[2023-03-15 16:26:16,523] [INFO] Task started: Blastn
[2023-03-15 16:26:16,523] [INFO] Running command: blastn -query OceanDNA-b31616/markers.fasta -db /var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference/reference_markers.fasta -out OceanDNA-b31616/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:17,401] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:17,416] [INFO] Selected 12 target genomes.
[2023-03-15 16:26:17,416] [INFO] Target genome list was writen to OceanDNA-b31616/target_genomes.txt
[2023-03-15 16:26:17,423] [INFO] Task started: fastANI
[2023-03-15 16:26:17,424] [INFO] Running command: fastANI --query /var/lib/cwl/stga49139ac-57b3-48e8-bfba-99fb9a475a08/OceanDNA-b31616.fa --refList OceanDNA-b31616/target_genomes.txt --output OceanDNA-b31616/fastani_result.tsv --threads 1
[2023-03-15 16:26:25,465] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:25,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:25,466] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:25,474] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:25,474] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:26:25,474] [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	84.6662	715	936	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	84.5543	702	936	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	84.4709	704	936	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.5933	463	936	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	79.3962	434	936	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.2646	403	936	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.0534	394	936	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.027	394	936	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.9489	413	936	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.9087	428	936	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.8542	334	936	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.5974	378	936	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:26:25,477] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31616/tc_result.tsv
[2023-03-15 16:26:25,483] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:25,483] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:25,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference/checkm_data
[2023-03-15 16:26:25,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:25,497] [INFO] Task started: CheckM
[2023-03-15 16:26:25,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31616/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31616/checkm_input OceanDNA-b31616/checkm_result
[2023-03-15 16:27:10,403] [INFO] Task succeeded: CheckM
[2023-03-15 16:27:10,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:27:10,458] [INFO] ===== Completeness check finished =====
[2023-03-15 16:27:10,458] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:27:10,458] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31616/markers.fasta)
[2023-03-15 16:27:10,460] [INFO] Task started: Blastn
[2023-03-15 16:27:10,460] [INFO] Running command: blastn -query OceanDNA-b31616/markers.fasta -db /var/lib/cwl/stg7e687460-f06b-409b-a7e6-0b58441e89c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31616/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:27:12,147] [INFO] Task succeeded: Blastn
[2023-03-15 16:27:12,157] [INFO] Selected 8 target genomes.
[2023-03-15 16:27:12,157] [INFO] Target genome list was writen to OceanDNA-b31616/target_genomes_gtdb.txt
[2023-03-15 16:27:12,166] [INFO] Task started: fastANI
[2023-03-15 16:27:12,166] [INFO] Running command: fastANI --query /var/lib/cwl/stga49139ac-57b3-48e8-bfba-99fb9a475a08/OceanDNA-b31616.fa --refList OceanDNA-b31616/target_genomes_gtdb.txt --output OceanDNA-b31616/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:27:17,742] [INFO] Task succeeded: fastANI
[2023-03-15 16:27:17,748] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:27:17,748] [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_002377695.1	s__Alteriqipengyuania sp002377695	99.9875	927	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_000186705.1	s__Alteriqipengyuania sp000186705	94.6587	847	936	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	84.8462	388	936	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	84.4991	704	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_003363135.1	s__Alteriqipengyuania lutimaris	84.4815	703	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	84.4414	705	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993635.1	s__Alteriqipengyuania sp009993635	84.0118	698	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.91	99.91	0.97	0.97	2	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	83.4978	662	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-15 16:27:17,756] [INFO] GTDB search result was written to OceanDNA-b31616/result_gtdb.tsv
[2023-03-15 16:27:17,773] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:27:17,784] [INFO] DFAST_QC result json was written to OceanDNA-b31616/dqc_result.json
[2023-03-15 16:27:17,784] [INFO] DFAST_QC completed!
[2023-03-15 16:27:17,784] [INFO] Total running time: 0h1m21s