[2024-01-24 14:22:58,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:58,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:58,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference
[2024-01-24 14:23:01,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:01,560] [INFO] Task started: Prodigal
[2024-01-24 14:23:01,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe341961-64b7-4c49-b598-62172df6877a/GCF_003940805.1_ASM394080v1_genomic.fna.gz | prodigal -d GCF_003940805.1_ASM394080v1_genomic.fna/cds.fna -a GCF_003940805.1_ASM394080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:16,204] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:16,205] [INFO] Task started: HMMsearch
[2024-01-24 14:23:16,205] [INFO] Running command: hmmsearch --tblout GCF_003940805.1_ASM394080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference/reference_markers.hmm GCF_003940805.1_ASM394080v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:16,570] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:16,571] [INFO] Found 6/6 markers.
[2024-01-24 14:23:16,620] [INFO] Query marker FASTA was written to GCF_003940805.1_ASM394080v1_genomic.fna/markers.fasta
[2024-01-24 14:23:16,620] [INFO] Task started: Blastn
[2024-01-24 14:23:16,620] [INFO] Running command: blastn -query GCF_003940805.1_ASM394080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference/reference_markers.fasta -out GCF_003940805.1_ASM394080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:20,538] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:20,542] [INFO] Selected 17 target genomes.
[2024-01-24 14:23:20,543] [INFO] Target genome list was writen to GCF_003940805.1_ASM394080v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:20,561] [INFO] Task started: fastANI
[2024-01-24 14:23:20,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe341961-64b7-4c49-b598-62172df6877a/GCF_003940805.1_ASM394080v1_genomic.fna.gz --refList GCF_003940805.1_ASM394080v1_genomic.fna/target_genomes.txt --output GCF_003940805.1_ASM394080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:36,442] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:36,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:36,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:36,463] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:36,463] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:36,463] [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
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	81.5861	798	1460	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	81.4784	792	1460	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	81.0885	812	1460	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	80.5243	645	1460	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	80.5039	645	1460	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.745	561	1460	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.2638	595	1460	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	79.2353	600	1460	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	79.1314	596	1460	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	79.0813	575	1460	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.8825	558	1460	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	78.8658	526	1460	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.7642	453	1460	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.6707	562	1460	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.2106	416	1460	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	78.0216	412	1460	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	77.9815	466	1460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:36,467] [INFO] DFAST Taxonomy check result was written to GCF_003940805.1_ASM394080v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:36,468] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:36,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:36,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference/checkm_data
[2024-01-24 14:23:36,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:36,526] [INFO] Task started: CheckM
[2024-01-24 14:23:36,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003940805.1_ASM394080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003940805.1_ASM394080v1_genomic.fna/checkm_input GCF_003940805.1_ASM394080v1_genomic.fna/checkm_result
[2024-01-24 14:24:32,285] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:32,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:32,314] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:32,314] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:32,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003940805.1_ASM394080v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:32,315] [INFO] Task started: Blastn
[2024-01-24 14:24:32,316] [INFO] Running command: blastn -query GCF_003940805.1_ASM394080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36aeefdd-fe1f-49f1-aea5-bb78dd88cf29/dqc_reference/reference_markers_gtdb.fasta -out GCF_003940805.1_ASM394080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:34,033] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:34,037] [INFO] Selected 21 target genomes.
[2024-01-24 14:24:34,038] [INFO] Target genome list was writen to GCF_003940805.1_ASM394080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:34,057] [INFO] Task started: fastANI
[2024-01-24 14:24:34,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe341961-64b7-4c49-b598-62172df6877a/GCF_003940805.1_ASM394080v1_genomic.fna.gz --refList GCF_003940805.1_ASM394080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003940805.1_ASM394080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:52,607] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:52,676] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:52,677] [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_003940805.1	s__Tabrizicola piscis	100.0	1460	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012036325.1	s__Tabrizicola sp012036325	84.3193	740	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821825.1	s__Tabrizicola sp013821825	82.3816	807	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	82.0983	887	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574395.1	s__Tabrizicola thermarum	81.5767	800	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	97.33	97.31	0.93	0.92	4	-
GCA_018057165.1	s__Tabrizicola sp018057165	81.4708	550	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999335.1	s__Tabrizicola soli	81.3763	799	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222785.1	s__Tabrizicola sp005222785	81.3026	867	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917595.1	s__Tabrizicola sp903917595	80.9166	674	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793705.1	s__Tabrizicola sp016793705	80.8813	783	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792905.1	s__Tabrizicola sp016792905	80.8191	744	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280405.1	s__Tabrizicola sp002280405	80.6731	611	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792685.1	s__Tabrizicola sp016792685	80.556	688	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859945.1	s__UBA1943 sp014859945	80.0275	526	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	79.7737	559	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	79.7645	649	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855575.1	s__Gemmobacter_B sp002855575	79.6049	656	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032275.1	s__JAAURK01 sp012032275	79.5583	564	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAURK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256185.1	s__Gemmobacter_B sp002256185	79.2822	540	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380135.2	s__Fertoeibacter niger	79.0067	630	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	78.9926	546	1460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:52,678] [INFO] GTDB search result was written to GCF_003940805.1_ASM394080v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:52,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:52,687] [INFO] DFAST_QC result json was written to GCF_003940805.1_ASM394080v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:52,688] [INFO] DFAST_QC completed!
[2024-01-24 14:24:52,688] [INFO] Total running time: 0h1m54s