[2024-01-24 13:22:30,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:30,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:30,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference
[2024-01-24 13:22:32,156] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,164] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg94ebf678-3769-4189-a5a8-89a97fa7b1df/GCF_002871005.1_ASM287100v1_genomic.fna.gz | prodigal -d GCF_002871005.1_ASM287100v1_genomic.fna/cds.fna -a GCF_002871005.1_ASM287100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:46,995] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:46,995] [INFO] Task started: HMMsearch
[2024-01-24 13:22:46,995] [INFO] Running command: hmmsearch --tblout GCF_002871005.1_ASM287100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference/reference_markers.hmm GCF_002871005.1_ASM287100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:47,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:47,277] [INFO] Found 6/6 markers.
[2024-01-24 13:22:47,323] [INFO] Query marker FASTA was written to GCF_002871005.1_ASM287100v1_genomic.fna/markers.fasta
[2024-01-24 13:22:47,323] [INFO] Task started: Blastn
[2024-01-24 13:22:47,323] [INFO] Running command: blastn -query GCF_002871005.1_ASM287100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference/reference_markers.fasta -out GCF_002871005.1_ASM287100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:48,346] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:48,349] [INFO] Selected 26 target genomes.
[2024-01-24 13:22:48,350] [INFO] Target genome list was writen to GCF_002871005.1_ASM287100v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:48,979] [INFO] Task started: fastANI
[2024-01-24 13:22:48,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ebf678-3769-4189-a5a8-89a97fa7b1df/GCF_002871005.1_ASM287100v1_genomic.fna.gz --refList GCF_002871005.1_ASM287100v1_genomic.fna/target_genomes.txt --output GCF_002871005.1_ASM287100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:09,389] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:09,390] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:09,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:09,413] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:23:09,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:23:09,413] [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
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	81.8359	831	1721	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	81.8097	837	1721	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.462	614	1721	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.3979	652	1721	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	79.3569	588	1721	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	79.2247	588	1721	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	79.2094	600	1721	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.7909	584	1721	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.7736	586	1721	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.6965	527	1721	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	78.5952	514	1721	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	78.5474	505	1721	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	78.5141	503	1721	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4764	495	1721	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.4425	469	1721	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.4339	471	1721	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	78.4314	557	1721	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	78.4252	426	1721	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	78.4126	554	1721	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.3817	628	1721	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0521	397	1721	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8329	428	1721	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6694	407	1721	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.6623	451	1721	95	below_threshold
Haematobacter massiliensis	strain=CCUG 47968	GCA_000740795.1	195105	195105	type	True	77.5681	300	1721	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.3704	364	1721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:09,415] [INFO] DFAST Taxonomy check result was written to GCF_002871005.1_ASM287100v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:09,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:09,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:09,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference/checkm_data
[2024-01-24 13:23:09,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:09,472] [INFO] Task started: CheckM
[2024-01-24 13:23:09,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002871005.1_ASM287100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002871005.1_ASM287100v1_genomic.fna/checkm_input GCF_002871005.1_ASM287100v1_genomic.fna/checkm_result
[2024-01-24 13:23:58,043] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:58,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:58,065] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:58,065] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:58,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002871005.1_ASM287100v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:58,066] [INFO] Task started: Blastn
[2024-01-24 13:23:58,066] [INFO] Running command: blastn -query GCF_002871005.1_ASM287100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6914ae39-5c6d-4eda-aa20-47488ecac966/dqc_reference/reference_markers_gtdb.fasta -out GCF_002871005.1_ASM287100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:59,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:59,807] [INFO] Selected 21 target genomes.
[2024-01-24 13:23:59,807] [INFO] Target genome list was writen to GCF_002871005.1_ASM287100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:00,747] [INFO] Task started: fastANI
[2024-01-24 13:24:00,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg94ebf678-3769-4189-a5a8-89a97fa7b1df/GCF_002871005.1_ASM287100v1_genomic.fna.gz --refList GCF_002871005.1_ASM287100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002871005.1_ASM287100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:18,341] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:18,360] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:18,361] [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_002871005.1	s__Acidimangrovimonas sediminis	100.0	1718	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106675.1	s__Acidimangrovimonas indica	81.7774	841	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004010155.1	s__Solirhodobacter olei	79.5898	738	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	79.3612	587	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	79.3355	633	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.946	514	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.8076	583	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	78.6983	531	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.5945	484	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	78.5623	513	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_002020355.1	s__Thioclava sediminum	78.5584	503	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	-
GCF_000442255.1	s__Salipiger mucosus	78.5263	587	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940525.2	s__Thioclava nitratireducens	78.5198	501	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
GCF_004923205.2	s__Paracoccus aeridis	78.4503	422	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	78.44	556	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015487335.1	s__S012-89 sp015487335	78.4304	334	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	78.4024	624	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009649175.1	s__Rhodovulum strictum	78.3704	468	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001691415.1	s__Pararhodobacter sp001691415	78.1814	527	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129775.1	s__Rhodobaculum sp007129775	77.917	274	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359765.1	s__Roseovarius sp014359765	77.85	372	1721	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:18,362] [INFO] GTDB search result was written to GCF_002871005.1_ASM287100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:18,363] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:18,370] [INFO] DFAST_QC result json was written to GCF_002871005.1_ASM287100v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:18,370] [INFO] DFAST_QC completed!
[2024-01-24 13:24:18,370] [INFO] Total running time: 0h1m48s