[2023-03-14 13:37:53,261] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:37:53,262] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:37:53,263] [INFO] DQC Reference Directory: /var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference
[2023-03-14 13:37:55,234] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:37:55,238] [INFO] Task started: Prodigal
[2023-03-14 13:37:55,239] [INFO] Running command: cat /var/lib/cwl/stg4227439d-0db0-4c0c-b298-e7e35f69acc1/OceanDNA-b36683.fa | prodigal -d OceanDNA-b36683/cds.fna -a OceanDNA-b36683/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:38:22,462] [INFO] Task succeeded: Prodigal
[2023-03-14 13:38:22,462] [INFO] Task started: HMMsearch
[2023-03-14 13:38:22,462] [INFO] Running command: hmmsearch --tblout OceanDNA-b36683/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference/reference_markers.hmm OceanDNA-b36683/protein.faa > /dev/null
[2023-03-14 13:38:22,683] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:38:22,683] [INFO] Found 6/6 markers.
[2023-03-14 13:38:22,705] [INFO] Query marker FASTA was written to OceanDNA-b36683/markers.fasta
[2023-03-14 13:38:22,705] [INFO] Task started: Blastn
[2023-03-14 13:38:22,705] [INFO] Running command: blastn -query OceanDNA-b36683/markers.fasta -db /var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference/reference_markers.fasta -out OceanDNA-b36683/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:38:23,454] [INFO] Task succeeded: Blastn
[2023-03-14 13:38:23,455] [INFO] Selected 21 target genomes.
[2023-03-14 13:38:23,456] [INFO] Target genome list was writen to OceanDNA-b36683/target_genomes.txt
[2023-03-14 13:38:23,487] [INFO] Task started: fastANI
[2023-03-14 13:38:23,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg4227439d-0db0-4c0c-b298-e7e35f69acc1/OceanDNA-b36683.fa --refList OceanDNA-b36683/target_genomes.txt --output OceanDNA-b36683/fastani_result.tsv --threads 1
[2023-03-14 13:38:38,972] [INFO] Task succeeded: fastANI
[2023-03-14 13:38:38,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:38:38,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:38:38,984] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 13:38:38,984] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 13:38:38,984] [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
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	96.7422	1091	1218	95	conclusive
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	80.2492	658	1218	95	below_threshold
Marinimicrobium alkaliphilum	strain=SW121	GCA_003259155.1	2202654	2202654	type	True	77.5451	302	1218	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	77.2391	154	1218	95	below_threshold
Microbulbifer mangrovi	strain=DD-13	GCA_002009015.1	927787	927787	type	True	77.2304	117	1218	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	77.0387	146	1218	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	77.0255	152	1218	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.7885	87	1218	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.7511	120	1218	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.7204	101	1218	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.714	97	1218	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	76.7108	120	1218	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.6889	96	1218	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.6666	92	1218	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.6309	95	1218	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	76.6182	123	1218	95	below_threshold
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	76.5518	127	1218	95	below_threshold
Exilibacterium tricleocarpae	strain=R142	GCA_007004655.1	2591008	2591008	type	True	76.0396	130	1218	95	below_threshold
Ferrimonas kyonanensis	strain=DSM 18153	GCA_000425405.1	364763	364763	type	True	75.7764	59	1218	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:38:38,984] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36683/tc_result.tsv
[2023-03-14 13:38:38,984] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:38:38,984] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:38:38,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference/checkm_data
[2023-03-14 13:38:38,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:38:39,120] [INFO] Task started: CheckM
[2023-03-14 13:38:39,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36683/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36683/checkm_input OceanDNA-b36683/checkm_result
[2023-03-14 13:39:50,395] [INFO] Task succeeded: CheckM
[2023-03-14 13:39:50,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:39:50,398] [INFO] ===== Completeness check finished =====
[2023-03-14 13:39:50,399] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:39:50,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36683/markers.fasta)
[2023-03-14 13:39:50,400] [INFO] Task started: Blastn
[2023-03-14 13:39:50,400] [INFO] Running command: blastn -query OceanDNA-b36683/markers.fasta -db /var/lib/cwl/stg74a59430-8c10-41c1-9c4c-aa9e23428ac0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36683/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:39:51,714] [INFO] Task succeeded: Blastn
[2023-03-14 13:39:51,715] [INFO] Selected 19 target genomes.
[2023-03-14 13:39:51,715] [INFO] Target genome list was writen to OceanDNA-b36683/target_genomes_gtdb.txt
[2023-03-14 13:39:51,728] [INFO] Task started: fastANI
[2023-03-14 13:39:51,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg4227439d-0db0-4c0c-b298-e7e35f69acc1/OceanDNA-b36683.fa --refList OceanDNA-b36683/target_genomes_gtdb.txt --output OceanDNA-b36683/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:40:16,081] [INFO] Task succeeded: fastANI
[2023-03-14 13:40:16,096] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:40:16,096] [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_003762925.1	s__Marinimicrobium koreense	96.7422	1091	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	96.56	95.81	0.88	0.87	5	conclusive
GCF_000423345.1	s__Marinimicrobium agarilyticum	80.2405	659	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259155.1	s__Marinimicrobium_A alkaliphilum	77.5561	301	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Marinimicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002959965.1	s__Microbulbifer pacificus	77.3341	142	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	77.2391	154	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	77.1958	159	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	77.025	152	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129095.1	s__Microbulbifer donghaiensis	77.0051	145	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305785.2	s__Simiduia agarivorans	76.7108	120	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011602365.1	s__Pseudomaricurvus hydrocarbonicus	76.6612	98	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	76.6182	123	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019225.1	s__Cellvibrio japonicus	76.5531	128	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	100.00	100.00	1.00	1.00	4	-
GCA_003634075.1	s__Teredinibacter sp003634075	76.4855	128	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Teredinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	76.3445	94	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004655.1	s__Exilibacterium tricleocarpae	76.0396	130	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Exilibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491205.1	s__Chimaeribacter sp005491205	75.8516	61	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chimaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425405.1	s__Ferrimonas kyonanensis	75.7764	59	1218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:40:16,097] [INFO] GTDB search result was written to OceanDNA-b36683/result_gtdb.tsv
[2023-03-14 13:40:16,109] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:40:16,111] [INFO] DFAST_QC result json was written to OceanDNA-b36683/dqc_result.json
[2023-03-14 13:40:16,112] [INFO] DFAST_QC completed!
[2023-03-14 13:40:16,112] [INFO] Total running time: 0h2m23s