[2024-01-24 12:22:13,978] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:13,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:13,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference
[2024-01-24 12:22:15,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,493] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,493] [INFO] Running command: gunzip -c /var/lib/cwl/stga2e5c2d5-76db-45a8-bdbd-c84f973bcc89/GCF_000299575.1_ASM29957v1_genomic.fna.gz | prodigal -d GCF_000299575.1_ASM29957v1_genomic.fna/cds.fna -a GCF_000299575.1_ASM29957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:24,331] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:24,331] [INFO] Task started: HMMsearch
[2024-01-24 12:22:24,331] [INFO] Running command: hmmsearch --tblout GCF_000299575.1_ASM29957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference/reference_markers.hmm GCF_000299575.1_ASM29957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:24,644] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:24,645] [INFO] Found 6/6 markers.
[2024-01-24 12:22:24,679] [INFO] Query marker FASTA was written to GCF_000299575.1_ASM29957v1_genomic.fna/markers.fasta
[2024-01-24 12:22:24,689] [INFO] Task started: Blastn
[2024-01-24 12:22:24,689] [INFO] Running command: blastn -query GCF_000299575.1_ASM29957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference/reference_markers.fasta -out GCF_000299575.1_ASM29957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:25,686] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:25,690] [INFO] Selected 27 target genomes.
[2024-01-24 12:22:25,690] [INFO] Target genome list was writen to GCF_000299575.1_ASM29957v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:25,707] [INFO] Task started: fastANI
[2024-01-24 12:22:25,707] [INFO] Running command: fastANI --query /var/lib/cwl/stga2e5c2d5-76db-45a8-bdbd-c84f973bcc89/GCF_000299575.1_ASM29957v1_genomic.fna.gz --refList GCF_000299575.1_ASM29957v1_genomic.fna/target_genomes.txt --output GCF_000299575.1_ASM29957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:44,593] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:44,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:44,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:44,618] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:44,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:44,618] [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
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	79.451	473	936	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.3055	464	936	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.1995	491	936	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.145	436	936	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.848	406	936	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	78.6931	428	936	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	78.6542	406	936	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	78.6283	401	936	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5381	423	936	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.4999	413	936	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	78.4285	349	936	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.3903	352	936	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	78.2838	365	936	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.25	376	936	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.1767	376	936	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	78.1723	342	936	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	78.1718	341	936	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	78.1322	375	936	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	78.0974	364	936	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.0834	408	936	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.0694	358	936	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.8623	376	936	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	77.8447	287	936	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	77.6369	369	936	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	77.6148	374	936	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.5658	292	936	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.433	227	936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:44,620] [INFO] DFAST Taxonomy check result was written to GCF_000299575.1_ASM29957v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:44,620] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:44,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:44,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference/checkm_data
[2024-01-24 12:22:44,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:44,654] [INFO] Task started: CheckM
[2024-01-24 12:22:44,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000299575.1_ASM29957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000299575.1_ASM29957v1_genomic.fna/checkm_input GCF_000299575.1_ASM29957v1_genomic.fna/checkm_result
[2024-01-24 12:23:17,335] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:17,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,356] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:17,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:17,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000299575.1_ASM29957v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:17,357] [INFO] Task started: Blastn
[2024-01-24 12:23:17,357] [INFO] Running command: blastn -query GCF_000299575.1_ASM29957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6211d8fb-1959-410c-b2cd-5718b1d9620c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000299575.1_ASM29957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,139] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,143] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:19,144] [INFO] Target genome list was writen to GCF_000299575.1_ASM29957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:19,170] [INFO] Task started: fastANI
[2024-01-24 12:23:19,171] [INFO] Running command: fastANI --query /var/lib/cwl/stga2e5c2d5-76db-45a8-bdbd-c84f973bcc89/GCF_000299575.1_ASM29957v1_genomic.fna.gz --refList GCF_000299575.1_ASM29957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000299575.1_ASM29957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:36,670] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,693] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:36,694] [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_000299575.1	s__Palleronia guishaninsula	100.0	935	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004358695.1	s__Palleronia sp004358695	79.4714	471	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	79.3997	483	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	79.2569	465	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	79.2036	490	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	79.1674	433	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.9262	462	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.8052	411	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002751875.1	s__Oceaniglobus indicus	78.772	413	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	78.6445	436	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	78.6078	403	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002865605.1	s__Paracoccus jeotgali	78.4287	349	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.34	96.34	0.97	0.97	2	-
GCF_009835145.1	s__Profundibacterium mesophilum	78.3994	390	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302445.1	s__Palleronia abyssalis	78.2997	383	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	78.2816	388	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	78.2816	365	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	78.2557	403	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_017315735.1	s__Paracoccus sp017315735	78.2193	379	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	78.1732	354	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.1701	378	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188295.1	s__Paracoccus sediminis	78.1399	345	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003340555.1	s__Jannaschia formosa	78.0759	409	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	77.9243	355	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	77.5993	376	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,695] [INFO] GTDB search result was written to GCF_000299575.1_ASM29957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:36,696] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:36,701] [INFO] DFAST_QC result json was written to GCF_000299575.1_ASM29957v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:36,701] [INFO] DFAST_QC completed!
[2024-01-24 12:23:36,701] [INFO] Total running time: 0h1m23s