[2024-01-24 13:19:11,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:11,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:11,469] [INFO] DQC Reference Directory: /var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference
[2024-01-24 13:19:12,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:12,718] [INFO] Task started: Prodigal
[2024-01-24 13:19:12,718] [INFO] Running command: gunzip -c /var/lib/cwl/stg2fc18099-6f50-4974-a0a0-7c03ff24198d/GCF_008086115.1_ASM808611v1_genomic.fna.gz | prodigal -d GCF_008086115.1_ASM808611v1_genomic.fna/cds.fna -a GCF_008086115.1_ASM808611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:24,165] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:24,166] [INFO] Task started: HMMsearch
[2024-01-24 13:19:24,166] [INFO] Running command: hmmsearch --tblout GCF_008086115.1_ASM808611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference/reference_markers.hmm GCF_008086115.1_ASM808611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:24,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:24,509] [INFO] Found 6/6 markers.
[2024-01-24 13:19:24,547] [INFO] Query marker FASTA was written to GCF_008086115.1_ASM808611v1_genomic.fna/markers.fasta
[2024-01-24 13:19:24,548] [INFO] Task started: Blastn
[2024-01-24 13:19:24,548] [INFO] Running command: blastn -query GCF_008086115.1_ASM808611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference/reference_markers.fasta -out GCF_008086115.1_ASM808611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:25,729] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:25,734] [INFO] Selected 28 target genomes.
[2024-01-24 13:19:25,735] [INFO] Target genome list was writen to GCF_008086115.1_ASM808611v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:25,759] [INFO] Task started: fastANI
[2024-01-24 13:19:25,760] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc18099-6f50-4974-a0a0-7c03ff24198d/GCF_008086115.1_ASM808611v1_genomic.fna.gz --refList GCF_008086115.1_ASM808611v1_genomic.fna/target_genomes.txt --output GCF_008086115.1_ASM808611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:47,746] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:47,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:47,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:47,771] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:47,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:47,771] [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
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	79.9339	552	1162	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	79.8716	562	1162	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	79.7737	592	1162	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	79.6148	540	1162	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.497	492	1162	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.4274	521	1162	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.3739	507	1162	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	79.2868	509	1162	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	79.257	490	1162	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.1894	482	1162	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.1629	512	1162	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.1476	500	1162	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.9869	408	1162	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.9158	516	1162	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.9007	490	1162	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.8262	488	1162	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.7204	429	1162	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6468	424	1162	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.6206	467	1162	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	78.4294	402	1162	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	78.3503	413	1162	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	78.2936	412	1162	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	78.2769	394	1162	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	78.2497	400	1162	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	78.2085	389	1162	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	78.2078	380	1162	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.2073	403	1162	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6201	383	1162	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,774] [INFO] DFAST Taxonomy check result was written to GCF_008086115.1_ASM808611v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:47,775] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:47,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:47,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference/checkm_data
[2024-01-24 13:19:47,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:47,820] [INFO] Task started: CheckM
[2024-01-24 13:19:47,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008086115.1_ASM808611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008086115.1_ASM808611v1_genomic.fna/checkm_input GCF_008086115.1_ASM808611v1_genomic.fna/checkm_result
[2024-01-24 13:20:27,362] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:27,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:27,386] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:27,387] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:27,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008086115.1_ASM808611v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:27,388] [INFO] Task started: Blastn
[2024-01-24 13:20:27,388] [INFO] Running command: blastn -query GCF_008086115.1_ASM808611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged32e792-22f3-4c1e-b616-f6123f3b2f09/dqc_reference/reference_markers_gtdb.fasta -out GCF_008086115.1_ASM808611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:29,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:29,426] [INFO] Selected 17 target genomes.
[2024-01-24 13:20:29,426] [INFO] Target genome list was writen to GCF_008086115.1_ASM808611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:29,461] [INFO] Task started: fastANI
[2024-01-24 13:20:29,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fc18099-6f50-4974-a0a0-7c03ff24198d/GCF_008086115.1_ASM808611v1_genomic.fna.gz --refList GCF_008086115.1_ASM808611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008086115.1_ASM808611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:41,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:41,866] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:41,866] [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_008086115.1	s__Muriiphilus fusiformis	100.0	1162	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	98.34	98.34	0.92	0.92	2	conclusive
GCF_014640115.1	s__Muriiphilus lacisalsi	81.1485	664	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177545.1	s__Muriiphilus sp900177545	80.6701	648	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694465.1	s__Muriiphilus sp003694465	80.1696	321	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152805.1	s__Maritimibacter alkaliphilus	79.9584	550	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCA_001873585.1	s__Muriiphilus sp001873585	79.8586	344	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.8401	547	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	79.7734	593	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	79.5331	483	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_900109035.1	s__Cribrihabitans marinus	79.4018	503	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002695005.1	s__Maritimibacter sp002695005	79.2406	525	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009857745.1	s__Thalassobius mangrovi	79.1405	514	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	78.9329	514	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_003344785.1	s__Puniceibacterium profundi	78.8944	508	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.6296	466	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	78.4506	508	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003075.1	s__IMCC34051 sp013003075	78.0362	264	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:41,868] [INFO] GTDB search result was written to GCF_008086115.1_ASM808611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:41,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:41,873] [INFO] DFAST_QC result json was written to GCF_008086115.1_ASM808611v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:41,873] [INFO] DFAST_QC completed!
[2024-01-24 13:20:41,873] [INFO] Total running time: 0h1m30s