[2024-01-24 14:19:30,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:30,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:30,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference
[2024-01-24 14:19:31,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:31,359] [INFO] Task started: Prodigal
[2024-01-24 14:19:31,359] [INFO] Running command: gunzip -c /var/lib/cwl/stg8079bf64-c6bd-4579-a212-2735b2751ebb/GCF_002751875.1_ASM275187v1_genomic.fna.gz | prodigal -d GCF_002751875.1_ASM275187v1_genomic.fna/cds.fna -a GCF_002751875.1_ASM275187v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:42,731] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:42,731] [INFO] Task started: HMMsearch
[2024-01-24 14:19:42,731] [INFO] Running command: hmmsearch --tblout GCF_002751875.1_ASM275187v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference/reference_markers.hmm GCF_002751875.1_ASM275187v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:42,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:42,980] [INFO] Found 6/6 markers.
[2024-01-24 14:19:43,017] [INFO] Query marker FASTA was written to GCF_002751875.1_ASM275187v1_genomic.fna/markers.fasta
[2024-01-24 14:19:43,017] [INFO] Task started: Blastn
[2024-01-24 14:19:43,017] [INFO] Running command: blastn -query GCF_002751875.1_ASM275187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference/reference_markers.fasta -out GCF_002751875.1_ASM275187v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:43,974] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:43,978] [INFO] Selected 29 target genomes.
[2024-01-24 14:19:43,978] [INFO] Target genome list was writen to GCF_002751875.1_ASM275187v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:44,092] [INFO] Task started: fastANI
[2024-01-24 14:19:44,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg8079bf64-c6bd-4579-a212-2735b2751ebb/GCF_002751875.1_ASM275187v1_genomic.fna.gz --refList GCF_002751875.1_ASM275187v1_genomic.fna/target_genomes.txt --output GCF_002751875.1_ASM275187v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:04,951] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:04,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:04,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:04,974] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:04,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:04,975] [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
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	80.3235	658	1209	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	78.6542	470	1209	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	78.4326	465	1209	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.3444	383	1209	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.3163	370	1209	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.3156	357	1209	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	78.1755	349	1209	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.997	361	1209	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	77.9765	343	1209	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	77.9395	344	1209	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	77.9368	343	1209	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.9175	366	1209	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.8972	420	1209	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.884	381	1209	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.8657	367	1209	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	77.8485	314	1209	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.7757	314	1209	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.7618	391	1209	95	below_threshold
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	77.7588	258	1209	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.7372	414	1209	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.7371	389	1209	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	77.6385	369	1209	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.6309	367	1209	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	77.6106	373	1209	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	77.5565	283	1209	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	77.5527	370	1209	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.5423	253	1209	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.455	250	1209	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	77.2219	329	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:04,977] [INFO] DFAST Taxonomy check result was written to GCF_002751875.1_ASM275187v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:04,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:04,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:04,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference/checkm_data
[2024-01-24 14:20:04,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:05,019] [INFO] Task started: CheckM
[2024-01-24 14:20:05,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002751875.1_ASM275187v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002751875.1_ASM275187v1_genomic.fna/checkm_input GCF_002751875.1_ASM275187v1_genomic.fna/checkm_result
[2024-01-24 14:20:49,959] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:49,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:49,978] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:49,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:49,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002751875.1_ASM275187v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:49,979] [INFO] Task started: Blastn
[2024-01-24 14:20:49,979] [INFO] Running command: blastn -query GCF_002751875.1_ASM275187v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeaa36bac-9129-40fb-be02-416b147c2625/dqc_reference/reference_markers_gtdb.fasta -out GCF_002751875.1_ASM275187v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:51,479] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:51,483] [INFO] Selected 19 target genomes.
[2024-01-24 14:20:51,483] [INFO] Target genome list was writen to GCF_002751875.1_ASM275187v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:51,537] [INFO] Task started: fastANI
[2024-01-24 14:20:51,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg8079bf64-c6bd-4579-a212-2735b2751ebb/GCF_002751875.1_ASM275187v1_genomic.fna.gz --refList GCF_002751875.1_ASM275187v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002751875.1_ASM275187v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:04,745] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:04,760] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:04,761] [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_002751875.1	s__Oceaniglobus indicus	100.0	1208	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002869745.1	s__Oceaniglobus roseus	80.1344	685	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009992615.1	s__Oceaniglobus sp009992615	78.8543	323	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008085915.1	s__Oceaniglobus sp008085915	78.6421	532	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	78.6336	473	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	78.6213	464	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086115.1	s__Muriiphilus fusiformis	78.2863	403	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	98.34	98.34	0.92	0.92	2	-
GCF_003057885.1	s__Oceaniglobus ichthyenteri	78.2674	409	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	77.9815	361	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382265.1	s__Yoonia vestfoldensis	77.9533	342	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	77.9404	375	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302445.1	s__Palleronia abyssalis	77.9348	347	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	77.8013	256	1209	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_002158905.1	s__Yoonia vestfoldensis_B	77.7749	308	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359745.1	s__JACIYW01 sp014359745	77.7194	296	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350345.1	s__Rhodobaculum breve	77.5675	282	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	77.5538	289	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_003259905.1	s__Salipiger aestuarii	77.5375	372	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.58	99.38	0.94	0.92	5	-
GCA_003605175.1	s__IMCC34051 sp003605175	77.4915	365	1209	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 14:21:04,762] [INFO] GTDB search result was written to GCF_002751875.1_ASM275187v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:04,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:04,768] [INFO] DFAST_QC result json was written to GCF_002751875.1_ASM275187v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:04,768] [INFO] DFAST_QC completed!
[2024-01-24 14:21:04,768] [INFO] Total running time: 0h1m35s