[2023-03-17 02:03:49,489] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:49,489] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:49,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference
[2023-03-17 02:03:50,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:50,614] [INFO] Task started: Prodigal
[2023-03-17 02:03:50,615] [INFO] Running command: cat /var/lib/cwl/stg2cbbd123-c52c-4421-ba43-a6c4273cbd28/OceanDNA-b30004.fa | prodigal -d OceanDNA-b30004/cds.fna -a OceanDNA-b30004/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:04:14,880] [INFO] Task succeeded: Prodigal
[2023-03-17 02:04:14,880] [INFO] Task started: HMMsearch
[2023-03-17 02:04:14,880] [INFO] Running command: hmmsearch --tblout OceanDNA-b30004/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference/reference_markers.hmm OceanDNA-b30004/protein.faa > /dev/null
[2023-03-17 02:04:15,097] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:04:15,097] [INFO] Found 6/6 markers.
[2023-03-17 02:04:15,119] [INFO] Query marker FASTA was written to OceanDNA-b30004/markers.fasta
[2023-03-17 02:04:15,120] [INFO] Task started: Blastn
[2023-03-17 02:04:15,120] [INFO] Running command: blastn -query OceanDNA-b30004/markers.fasta -db /var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference/reference_markers.fasta -out OceanDNA-b30004/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:15,843] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:15,844] [INFO] Selected 18 target genomes.
[2023-03-17 02:04:15,844] [INFO] Target genome list was writen to OceanDNA-b30004/target_genomes.txt
[2023-03-17 02:04:15,856] [INFO] Task started: fastANI
[2023-03-17 02:04:15,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cbbd123-c52c-4421-ba43-a6c4273cbd28/OceanDNA-b30004.fa --refList OceanDNA-b30004/target_genomes.txt --output OceanDNA-b30004/fastani_result.tsv --threads 1
[2023-03-17 02:04:30,252] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:30,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:30,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:30,263] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 02:04:30,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 02:04:30,263] [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
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	99.947	1230	1267	95	conclusive
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	85.3143	1021	1267	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	79.9498	641	1267	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.541	620	1267	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.2341	606	1267	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.2142	616	1267	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.0653	617	1267	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.0621	612	1267	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.3694	474	1267	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.3108	464	1267	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.2166	451	1267	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.9666	419	1267	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.8826	417	1267	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.6347	311	1267	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	77.4377	330	1267	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.2556	253	1267	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.2156	216	1267	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.0387	236	1267	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:04:30,263] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30004/tc_result.tsv
[2023-03-17 02:04:30,263] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:30,263] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:30,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference/checkm_data
[2023-03-17 02:04:30,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:30,269] [INFO] Task started: CheckM
[2023-03-17 02:04:30,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30004/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30004/checkm_input OceanDNA-b30004/checkm_result
[2023-03-17 02:05:33,720] [INFO] Task succeeded: CheckM
[2023-03-17 02:05:33,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:05:33,723] [INFO] ===== Completeness check finished =====
[2023-03-17 02:05:33,723] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:05:33,724] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30004/markers.fasta)
[2023-03-17 02:05:33,725] [INFO] Task started: Blastn
[2023-03-17 02:05:33,725] [INFO] Running command: blastn -query OceanDNA-b30004/markers.fasta -db /var/lib/cwl/stg1db5b337-0377-4d58-a66b-450a7ff7e4d1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30004/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:05:34,918] [INFO] Task succeeded: Blastn
[2023-03-17 02:05:34,919] [INFO] Selected 12 target genomes.
[2023-03-17 02:05:34,919] [INFO] Target genome list was writen to OceanDNA-b30004/target_genomes_gtdb.txt
[2023-03-17 02:05:35,192] [INFO] Task started: fastANI
[2023-03-17 02:05:35,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cbbd123-c52c-4421-ba43-a6c4273cbd28/OceanDNA-b30004.fa --refList OceanDNA-b30004/target_genomes_gtdb.txt --output OceanDNA-b30004/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:05:45,608] [INFO] Task succeeded: fastANI
[2023-03-17 02:05:45,616] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:05:45,616] [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_003575965.1	s__Pseudooceanicola sediminis	99.947	1230	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	conclusive
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	85.3143	1021	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	79.9415	642	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.5308	616	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	79.5229	621	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	79.3659	639	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	79.2115	609	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	79.1368	579	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	79.0549	613	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015223355.1	s__Salipiger pacificus_B	78.1498	417	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	78.1121	380	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282555.1	s__EhC02 sp002282555	77.5503	162	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:05:45,616] [INFO] GTDB search result was written to OceanDNA-b30004/result_gtdb.tsv
[2023-03-17 02:05:45,616] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:05:45,618] [INFO] DFAST_QC result json was written to OceanDNA-b30004/dqc_result.json
[2023-03-17 02:05:45,618] [INFO] DFAST_QC completed!
[2023-03-17 02:05:45,618] [INFO] Total running time: 0h1m56s