[2024-01-24 10:47:06,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference
[2024-01-24 10:47:12,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stgd613110f-78fe-4564-9ab0-8b0d2b04bf8b/GCF_003688285.1_ASM368828v1_genomic.fna.gz | prodigal -d GCF_003688285.1_ASM368828v1_genomic.fna/cds.fna -a GCF_003688285.1_ASM368828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:23,997] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:23,997] [INFO] Task started: HMMsearch
[2024-01-24 10:47:23,997] [INFO] Running command: hmmsearch --tblout GCF_003688285.1_ASM368828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference/reference_markers.hmm GCF_003688285.1_ASM368828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,244] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,278] [INFO] Query marker FASTA was written to GCF_003688285.1_ASM368828v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,279] [INFO] Task started: Blastn
[2024-01-24 10:47:24,279] [INFO] Running command: blastn -query GCF_003688285.1_ASM368828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference/reference_markers.fasta -out GCF_003688285.1_ASM368828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,255] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,259] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:25,260] [INFO] Target genome list was writen to GCF_003688285.1_ASM368828v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,281] [INFO] Task started: fastANI
[2024-01-24 10:47:25,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgd613110f-78fe-4564-9ab0-8b0d2b04bf8b/GCF_003688285.1_ASM368828v1_genomic.fna.gz --refList GCF_003688285.1_ASM368828v1_genomic.fna/target_genomes.txt --output GCF_003688285.1_ASM368828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:37,818] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:37,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:37,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:37,832] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:37,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:37,833] [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
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	100.0	1268	1268	95	conclusive
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.7915	474	1268	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	78.3918	470	1268	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	78.124	476	1268	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	77.924	414	1268	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.845	353	1268	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.7405	347	1268	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.7375	380	1268	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.6695	363	1268	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.6396	318	1268	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.4343	305	1268	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.2909	331	1268	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.1617	301	1268	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.1347	276	1268	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.132	287	1268	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.1314	287	1268	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.115	233	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:37,835] [INFO] DFAST Taxonomy check result was written to GCF_003688285.1_ASM368828v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:37,836] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:37,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:37,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference/checkm_data
[2024-01-24 10:47:37,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:37,877] [INFO] Task started: CheckM
[2024-01-24 10:47:37,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688285.1_ASM368828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688285.1_ASM368828v1_genomic.fna/checkm_input GCF_003688285.1_ASM368828v1_genomic.fna/checkm_result
[2024-01-24 10:48:16,131] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:16,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,150] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:16,150] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:16,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688285.1_ASM368828v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:16,150] [INFO] Task started: Blastn
[2024-01-24 10:48:16,151] [INFO] Running command: blastn -query GCF_003688285.1_ASM368828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d2f3c3b-add7-4bbf-9a4b-5cc603d609c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688285.1_ASM368828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:17,882] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:17,887] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:17,887] [INFO] Target genome list was writen to GCF_003688285.1_ASM368828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:17,898] [INFO] Task started: fastANI
[2024-01-24 10:48:17,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgd613110f-78fe-4564-9ab0-8b0d2b04bf8b/GCF_003688285.1_ASM368828v1_genomic.fna.gz --refList GCF_003688285.1_ASM368828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688285.1_ASM368828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:30,316] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:30,330] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:30,330] [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_003688285.1	s__Rhodophyticola porphyridii	100.0	1268	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017644125.1	s__Rhodophyticola sp017644125	94.2957	1146	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_004751985.1	s__Rhodophyticola sp004751985	80.248	729	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827395.1	s__Rhodophyticola sp007827395	79.493	671	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	95.40	95.35	0.93	0.92	216	-
GCF_013155465.1	s__Alterinioella nitratireducens	78.6376	514	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCA_015689745.1	s__Roseicyclus sp015689745	78.6332	471	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.4361	526	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000255.1	s__Nioella ostreopsis	78.3764	472	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	78.2657	480	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401965.1	s__Roseicyclus sp018401965	78.2142	366	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	78.1339	444	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879695.1	s__Nioella sediminis	78.124	476	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	78.1094	474	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	77.9247	414	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	77.8636	416	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	77.7722	372	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.7488	346	1268	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:30,331] [INFO] GTDB search result was written to GCF_003688285.1_ASM368828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:30,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:30,335] [INFO] DFAST_QC result json was written to GCF_003688285.1_ASM368828v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:30,335] [INFO] DFAST_QC completed!
[2024-01-24 10:48:30,336] [INFO] Total running time: 0h1m24s