[2023-03-15 23:09:36,624] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:09:36,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:09:36,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference
[2023-03-15 23:09:37,727] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:09:37,728] [INFO] Task started: Prodigal
[2023-03-15 23:09:37,728] [INFO] Running command: cat /var/lib/cwl/stgd6d3e45e-d13d-4d99-8458-53f67474ef32/OceanDNA-b31578.fa | prodigal -d OceanDNA-b31578/cds.fna -a OceanDNA-b31578/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:09:49,837] [INFO] Task succeeded: Prodigal
[2023-03-15 23:09:49,837] [INFO] Task started: HMMsearch
[2023-03-15 23:09:49,837] [INFO] Running command: hmmsearch --tblout OceanDNA-b31578/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference/reference_markers.hmm OceanDNA-b31578/protein.faa > /dev/null
[2023-03-15 23:09:50,003] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:09:50,003] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6d3e45e-d13d-4d99-8458-53f67474ef32/OceanDNA-b31578.fa]
[2023-03-15 23:09:50,043] [INFO] Query marker FASTA was written to OceanDNA-b31578/markers.fasta
[2023-03-15 23:09:50,044] [INFO] Task started: Blastn
[2023-03-15 23:09:50,045] [INFO] Running command: blastn -query OceanDNA-b31578/markers.fasta -db /var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference/reference_markers.fasta -out OceanDNA-b31578/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:09:50,710] [INFO] Task succeeded: Blastn
[2023-03-15 23:09:50,710] [INFO] Selected 15 target genomes.
[2023-03-15 23:09:50,711] [INFO] Target genome list was writen to OceanDNA-b31578/target_genomes.txt
[2023-03-15 23:09:50,718] [INFO] Task started: fastANI
[2023-03-15 23:09:50,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d3e45e-d13d-4d99-8458-53f67474ef32/OceanDNA-b31578.fa --refList OceanDNA-b31578/target_genomes.txt --output OceanDNA-b31578/fastani_result.tsv --threads 1
[2023-03-15 23:09:58,945] [INFO] Task succeeded: fastANI
[2023-03-15 23:09:58,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:09:58,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:09:58,956] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:09:58,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:09:58,956] [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	84.5946	478	659	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	83.024	457	659	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	82.981	465	659	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.7117	253	659	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.5199	259	659	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.5088	197	659	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.4795	233	659	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.3778	242	659	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.3076	207	659	95	below_threshold
Qipengyuania sphaerica	strain=GH29	GCA_019711595.1	2867243	2867243	type	True	78.2612	213	659	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.1428	210	659	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.0742	206	659	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	78.0677	223	659	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	77.9456	190	659	95	below_threshold
Erythrobacter tepidarius	strain=DSM 10594	GCA_002155695.1	60454	60454	type	True	77.8477	222	659	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:09:58,956] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31578/tc_result.tsv
[2023-03-15 23:09:58,956] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:09:58,956] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:09:58,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference/checkm_data
[2023-03-15 23:09:58,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:09:58,961] [INFO] Task started: CheckM
[2023-03-15 23:09:58,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31578/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31578/checkm_input OceanDNA-b31578/checkm_result
[2023-03-15 23:10:32,434] [INFO] Task succeeded: CheckM
[2023-03-15 23:10:32,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.05%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:10:32,437] [INFO] ===== Completeness check finished =====
[2023-03-15 23:10:32,437] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:10:32,437] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31578/markers.fasta)
[2023-03-15 23:10:32,438] [INFO] Task started: Blastn
[2023-03-15 23:10:32,438] [INFO] Running command: blastn -query OceanDNA-b31578/markers.fasta -db /var/lib/cwl/stg8501b4ac-0f63-400e-b886-ef5358b720d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31578/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:10:33,500] [INFO] Task succeeded: Blastn
[2023-03-15 23:10:33,501] [INFO] Selected 7 target genomes.
[2023-03-15 23:10:33,501] [INFO] Target genome list was writen to OceanDNA-b31578/target_genomes_gtdb.txt
[2023-03-15 23:10:33,554] [INFO] Task started: fastANI
[2023-03-15 23:10:33,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6d3e45e-d13d-4d99-8458-53f67474ef32/OceanDNA-b31578.fa --refList OceanDNA-b31578/target_genomes_gtdb.txt --output OceanDNA-b31578/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:10:37,476] [INFO] Task succeeded: fastANI
[2023-03-15 23:10:37,481] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:10:37,481] [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	88.3987	498	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	84.582	467	659	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	84.5284	480	659	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	83.0298	442	659	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	82.9993	464	659	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	82.6878	446	659	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	82.6693	248	659	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:10:37,481] [INFO] GTDB search result was written to OceanDNA-b31578/result_gtdb.tsv
[2023-03-15 23:10:37,482] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:10:37,483] [INFO] DFAST_QC result json was written to OceanDNA-b31578/dqc_result.json
[2023-03-15 23:10:37,483] [INFO] DFAST_QC completed!
[2023-03-15 23:10:37,483] [INFO] Total running time: 0h1m1s