[2023-06-30 04:21:20,578] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:21:20,581] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:21:20,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference
[2023-06-30 04:21:22,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:21:22,850] [INFO] Task started: Prodigal
[2023-06-30 04:21:22,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg496fdae4-8ea3-4fb0-b440-8d43190e02c9/GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna.gz | prodigal -d GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/cds.fna -a GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:21:33,200] [INFO] Task succeeded: Prodigal
[2023-06-30 04:21:33,201] [INFO] Task started: HMMsearch
[2023-06-30 04:21:33,201] [INFO] Running command: hmmsearch --tblout GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference/reference_markers.hmm GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:21:33,459] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:21:33,461] [INFO] Found 6/6 markers.
[2023-06-30 04:21:33,494] [INFO] Query marker FASTA was written to GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/markers.fasta
[2023-06-30 04:21:33,494] [INFO] Task started: Blastn
[2023-06-30 04:21:33,494] [INFO] Running command: blastn -query GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/markers.fasta -db /var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference/reference_markers.fasta -out GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:21:34,408] [INFO] Task succeeded: Blastn
[2023-06-30 04:21:34,413] [INFO] Selected 25 target genomes.
[2023-06-30 04:21:34,414] [INFO] Target genome list was writen to GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/target_genomes.txt
[2023-06-30 04:21:34,428] [INFO] Task started: fastANI
[2023-06-30 04:21:34,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg496fdae4-8ea3-4fb0-b440-8d43190e02c9/GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna.gz --refList GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/target_genomes.txt --output GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:21:52,015] [INFO] Task succeeded: fastANI
[2023-06-30 04:21:52,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:21:52,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:21:52,039] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:21:52,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:21:52,040] [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
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	78.3537	402	1208	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.2185	412	1208	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	78.1858	409	1208	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	78.1692	381	1208	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	78.1244	378	1208	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	78.053	425	1208	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	78.0122	428	1208	95	below_threshold
Brevundimonas viscosa	strain=CGMCC 1.10683	GCA_900116065.1	871741	871741	type	True	78.0089	274	1208	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	77.9942	426	1208	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	77.9852	419	1208	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	77.9458	408	1208	95	below_threshold
Brevundimonas lenta	strain=DSM 23960	GCA_014196335.1	424796	424796	type	True	77.9271	270	1208	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	77.9171	408	1208	95	below_threshold
Brevundimonas mediterranea	strain=DSM 14878	GCA_014196125.1	74329	74329	type	True	77.9149	259	1208	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	77.7979	377	1208	95	below_threshold
Brevundimonas fluminis	strain=LA-55	GCA_003934285.1	2487274	2487274	type	True	77.783	258	1208	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	77.7373	262	1208	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.5626	271	1208	95	below_threshold
Brevundimonas naejangsanensis	strain=DSM 23858	GCA_000421705.1	588932	588932	type	True	77.5253	261	1208	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	77.5015	343	1208	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.1873	226	1208	95	below_threshold
Asticcacaulis endophyticus	strain=KCTC 32296	GCA_014652575.1	1395890	1395890	type	True	76.0556	81	1208	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	75.9938	220	1208	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.9732	218	1208	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.9398	220	1208	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:21:52,043] [INFO] DFAST Taxonomy check result was written to GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/tc_result.tsv
[2023-06-30 04:21:52,043] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:21:52,043] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:21:52,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference/checkm_data
[2023-06-30 04:21:52,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:21:52,084] [INFO] Task started: CheckM
[2023-06-30 04:21:52,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/checkm_input GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/checkm_result
[2023-06-30 04:22:24,968] [INFO] Task succeeded: CheckM
[2023-06-30 04:22:24,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:22:25,006] [INFO] ===== Completeness check finished =====
[2023-06-30 04:22:25,006] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:22:25,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/markers.fasta)
[2023-06-30 04:22:25,007] [INFO] Task started: Blastn
[2023-06-30 04:22:25,007] [INFO] Running command: blastn -query GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/markers.fasta -db /var/lib/cwl/stg93f45bab-42f4-435d-bb6d-6295a91321eb/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:22:26,780] [INFO] Task succeeded: Blastn
[2023-06-30 04:22:26,785] [INFO] Selected 21 target genomes.
[2023-06-30 04:22:26,786] [INFO] Target genome list was writen to GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:22:26,821] [INFO] Task started: fastANI
[2023-06-30 04:22:26,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg496fdae4-8ea3-4fb0-b440-8d43190e02c9/GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna.gz --refList GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/target_genomes_gtdb.txt --output GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:22:42,681] [INFO] Task succeeded: fastANI
[2023-06-30 04:22:42,707] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:22:42,708] [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_903862425.1	s__CAIOYC01 sp903862425	100.0	1206	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_903837135.1	s__CAIOYC01 sp903837135	81.3841	718	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIOYC01	95.0	99.97	99.97	0.97	0.97	3	-
GCA_017418605.1	s__CAISGS01 sp017418605	78.7252	448	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280485.1	s__NCED01 sp002280485	78.6965	324	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__NCED01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765965.1	s__CAHJWH01 sp009765965	78.6956	419	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAHJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903642205.1	s__CAHJWH01 sp903642205	78.4747	306	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAHJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	78.4563	446	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884425.1	s__CAIMFV01 sp903884425	78.3306	367	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.90	99.80	0.98	0.97	6	-
GCF_003254505.1	s__Phenylobacterium hankyongense	78.3106	406	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851655.1	s__CAIMFV01 sp903851655	78.2567	340	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.52	99.51	0.87	0.86	3	-
GCF_016467375.1	s__Caulobacter sp016467375	78.2167	330	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342605.1	s__Caulobacter sp004342605	78.1325	413	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975005.1	s__17J80-11 sp010975005	78.1313	339	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185805.1	s__Caulobacter sp003185805	78.1245	376	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929535.1	s__BOG-938 sp903929535	78.0293	272	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-938	95.0	99.86	99.86	0.89	0.89	2	-
GCA_004799515.1	s__Phenylobacterium sp004799515	78.0079	423	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234625.1	s__Caulobacter sp016234625	77.9638	328	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002749615.1	s__Caulobacter mirabilis	77.9507	406	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799545.1	s__Phenylobacterium sp004799545	77.928	372	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165275.1	s__BOG-935 sp003165275	77.901	365	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	77.5907	290	1208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:22:42,710] [INFO] GTDB search result was written to GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/result_gtdb.tsv
[2023-06-30 04:22:42,711] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:22:42,718] [INFO] DFAST_QC result json was written to GCA_903862425.1_freshwater_MAG_---_MJ-time_bin-8353_genomic.fna/dqc_result.json
[2023-06-30 04:22:42,718] [INFO] DFAST_QC completed!
[2023-06-30 04:22:42,719] [INFO] Total running time: 0h1m22s