[2023-06-27 11:41:29,733] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:41:29,736] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:41:29,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference
[2023-06-27 11:41:30,909] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:41:30,910] [INFO] Task started: Prodigal
[2023-06-27 11:41:30,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg125ca3df-6531-4cd7-9982-a71c581f7f04/GCA_026982255.1_ASM2698225v1_genomic.fna.gz | prodigal -d GCA_026982255.1_ASM2698225v1_genomic.fna/cds.fna -a GCA_026982255.1_ASM2698225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:41:37,261] [INFO] Task succeeded: Prodigal
[2023-06-27 11:41:37,261] [INFO] Task started: HMMsearch
[2023-06-27 11:41:37,261] [INFO] Running command: hmmsearch --tblout GCA_026982255.1_ASM2698225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference/reference_markers.hmm GCA_026982255.1_ASM2698225v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:41:37,511] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:41:37,512] [INFO] Found 6/6 markers.
[2023-06-27 11:41:37,535] [INFO] Query marker FASTA was written to GCA_026982255.1_ASM2698225v1_genomic.fna/markers.fasta
[2023-06-27 11:41:37,535] [INFO] Task started: Blastn
[2023-06-27 11:41:37,536] [INFO] Running command: blastn -query GCA_026982255.1_ASM2698225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference/reference_markers.fasta -out GCA_026982255.1_ASM2698225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:38,354] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:38,518] [INFO] Selected 29 target genomes.
[2023-06-27 11:41:38,518] [INFO] Target genome list was writen to GCA_026982255.1_ASM2698225v1_genomic.fna/target_genomes.txt
[2023-06-27 11:41:38,528] [INFO] Task started: fastANI
[2023-06-27 11:41:38,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg125ca3df-6531-4cd7-9982-a71c581f7f04/GCA_026982255.1_ASM2698225v1_genomic.fna.gz --refList GCA_026982255.1_ASM2698225v1_genomic.fna/target_genomes.txt --output GCA_026982255.1_ASM2698225v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:41:56,486] [INFO] Task succeeded: fastANI
[2023-06-27 11:41:56,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:41:56,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:41:56,508] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:41:56,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:41:56,508] [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
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	77.6562	220	665	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.5782	215	665	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.5758	216	665	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	77.5209	214	665	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	77.3235	181	665	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.2752	181	665	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.1871	195	665	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.1621	181	665	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.1552	185	665	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.1484	168	665	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.1427	186	665	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	77.0882	181	665	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	77.0611	181	665	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	77.0422	167	665	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	76.9076	192	665	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	76.8963	194	665	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	76.8637	147	665	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.8636	160	665	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	76.8319	163	665	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.8148	176	665	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.8126	145	665	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	76.7785	119	665	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	76.7456	167	665	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	76.7156	132	665	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	76.6713	117	665	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.5776	163	665	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	76.3519	87	665	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.3492	163	665	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	76.1789	65	665	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:41:56,510] [INFO] DFAST Taxonomy check result was written to GCA_026982255.1_ASM2698225v1_genomic.fna/tc_result.tsv
[2023-06-27 11:41:56,511] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:41:56,511] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:41:56,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference/checkm_data
[2023-06-27 11:41:56,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:41:56,537] [INFO] Task started: CheckM
[2023-06-27 11:41:56,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026982255.1_ASM2698225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026982255.1_ASM2698225v1_genomic.fna/checkm_input GCA_026982255.1_ASM2698225v1_genomic.fna/checkm_result
[2023-06-27 11:42:20,393] [INFO] Task succeeded: CheckM
[2023-06-27 11:42:20,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:42:20,418] [INFO] ===== Completeness check finished =====
[2023-06-27 11:42:20,418] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:42:20,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026982255.1_ASM2698225v1_genomic.fna/markers.fasta)
[2023-06-27 11:42:20,418] [INFO] Task started: Blastn
[2023-06-27 11:42:20,419] [INFO] Running command: blastn -query GCA_026982255.1_ASM2698225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg229a52d9-57fa-48bb-822c-2d76a32d462b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026982255.1_ASM2698225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:42:21,912] [INFO] Task succeeded: Blastn
[2023-06-27 11:42:21,918] [INFO] Selected 22 target genomes.
[2023-06-27 11:42:21,918] [INFO] Target genome list was writen to GCA_026982255.1_ASM2698225v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:42:21,928] [INFO] Task started: fastANI
[2023-06-27 11:42:21,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg125ca3df-6531-4cd7-9982-a71c581f7f04/GCA_026982255.1_ASM2698225v1_genomic.fna.gz --refList GCA_026982255.1_ASM2698225v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026982255.1_ASM2698225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:42:35,737] [INFO] Task succeeded: fastANI
[2023-06-27 11:42:35,754] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:42:35,755] [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_015485375.1	s__UBA3077 sp015485375	86.6626	445	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487165.1	s__UBA5972 sp015487165	78.007	190	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	77.6696	219	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013093415.1	s__Halovulum dunhuangense	77.5957	213	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	77.5617	217	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366645.1	s__UBA3077 sp002366645	77.436	138	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.3989	177	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746395.1	s__UBA3077 sp002746395	77.3806	168	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	77.291	217	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.2015	194	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	77.1775	180	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_000744955.1	s__Actibacterium sp000744955	77.1599	200	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	77.0745	175	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.0663	186	665	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	77.0488	177	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	77.0119	173	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.9542	156	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162875.1	s__UBA3077 sp002162875	76.9318	146	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	76.8952	158	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	76.8932	171	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765235.1	s__UBA3077 sp016765235	76.8809	161	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	76.3738	161	665	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:42:35,757] [INFO] GTDB search result was written to GCA_026982255.1_ASM2698225v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:42:35,760] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:42:35,765] [INFO] DFAST_QC result json was written to GCA_026982255.1_ASM2698225v1_genomic.fna/dqc_result.json
[2023-06-27 11:42:35,766] [INFO] DFAST_QC completed!
[2023-06-27 11:42:35,766] [INFO] Total running time: 0h1m6s