[2024-01-24 12:40:35,019] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:35,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:35,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference
[2024-01-24 12:40:36,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:36,261] [INFO] Task started: Prodigal
[2024-01-24 12:40:36,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg92a76a29-ad00-4fa6-9112-4f016b4b41b3/GCF_019297855.1_ASM1929785v1_genomic.fna.gz | prodigal -d GCF_019297855.1_ASM1929785v1_genomic.fna/cds.fna -a GCF_019297855.1_ASM1929785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:49,504] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:49,504] [INFO] Task started: HMMsearch
[2024-01-24 12:40:49,504] [INFO] Running command: hmmsearch --tblout GCF_019297855.1_ASM1929785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference/reference_markers.hmm GCF_019297855.1_ASM1929785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:49,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:49,763] [INFO] Found 6/6 markers.
[2024-01-24 12:40:49,792] [INFO] Query marker FASTA was written to GCF_019297855.1_ASM1929785v1_genomic.fna/markers.fasta
[2024-01-24 12:40:49,792] [INFO] Task started: Blastn
[2024-01-24 12:40:49,792] [INFO] Running command: blastn -query GCF_019297855.1_ASM1929785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference/reference_markers.fasta -out GCF_019297855.1_ASM1929785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:50,792] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:50,796] [INFO] Selected 26 target genomes.
[2024-01-24 12:40:50,796] [INFO] Target genome list was writen to GCF_019297855.1_ASM1929785v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:50,807] [INFO] Task started: fastANI
[2024-01-24 12:40:50,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg92a76a29-ad00-4fa6-9112-4f016b4b41b3/GCF_019297855.1_ASM1929785v1_genomic.fna.gz --refList GCF_019297855.1_ASM1929785v1_genomic.fna/target_genomes.txt --output GCF_019297855.1_ASM1929785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:09,308] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:09,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:09,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:09,340] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:41:09,340] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:41:09,341] [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
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.6543	428	1207	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.5494	461	1207	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.4089	403	1207	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	78.3515	395	1207	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	78.2001	420	1207	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.1955	363	1207	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	78.1926	410	1207	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.1573	362	1207	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.1492	441	1207	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.1415	397	1207	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	78.0988	360	1207	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	78.0866	334	1207	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	78.0181	396	1207	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	77.9942	429	1207	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9609	317	1207	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.9494	371	1207	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.8809	401	1207	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.7701	342	1207	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.7663	292	1207	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.7257	343	1207	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6645	298	1207	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.6122	294	1207	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6114	315	1207	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.6014	301	1207	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4648	316	1207	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.4178	306	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:09,342] [INFO] DFAST Taxonomy check result was written to GCF_019297855.1_ASM1929785v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:09,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:09,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:09,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference/checkm_data
[2024-01-24 12:41:09,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:09,381] [INFO] Task started: CheckM
[2024-01-24 12:41:09,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019297855.1_ASM1929785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019297855.1_ASM1929785v1_genomic.fna/checkm_input GCF_019297855.1_ASM1929785v1_genomic.fna/checkm_result
[2024-01-24 12:41:51,730] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:51,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:51,750] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:51,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:51,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019297855.1_ASM1929785v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:51,751] [INFO] Task started: Blastn
[2024-01-24 12:41:51,752] [INFO] Running command: blastn -query GCF_019297855.1_ASM1929785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg425d9214-ea4a-4973-8925-d34ccd12ba23/dqc_reference/reference_markers_gtdb.fasta -out GCF_019297855.1_ASM1929785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:53,597] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:53,602] [INFO] Selected 16 target genomes.
[2024-01-24 12:41:53,602] [INFO] Target genome list was writen to GCF_019297855.1_ASM1929785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:53,620] [INFO] Task started: fastANI
[2024-01-24 12:41:53,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg92a76a29-ad00-4fa6-9112-4f016b4b41b3/GCF_019297855.1_ASM1929785v1_genomic.fna.gz --refList GCF_019297855.1_ASM1929785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019297855.1_ASM1929785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:04,881] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:04,905] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:42:04,906] [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
GCA_019195455.1	s__Roseicyclus sp001650845	81.0589	830	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	96.25	96.25	0.88	0.88	2	-
GCA_015689645.1	s__Roseicyclus sp015689645	80.5607	694	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013565.1	s__Roseicyclus sp000013565	80.2105	753	1207	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	79.8063	575	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	79.3766	536	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	79.0529	484	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	78.5838	501	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	78.5647	456	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_000590925.1	s__Roseicyclus elongatus	78.5494	461	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763475.1	s__Roseicyclus sp016763475	78.3714	420	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.1957	363	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003340555.1	s__Jannaschia formosa	77.9712	433	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	77.9058	328	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	77.7529	347	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_004339675.1	s__Rhodovulum steppense	77.6014	301	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	77.3893	235	1207	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:04,907] [INFO] GTDB search result was written to GCF_019297855.1_ASM1929785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:04,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:04,912] [INFO] DFAST_QC result json was written to GCF_019297855.1_ASM1929785v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:04,912] [INFO] DFAST_QC completed!
[2024-01-24 12:42:04,913] [INFO] Total running time: 0h1m30s