[2024-01-24 12:37:24,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference
[2024-01-24 12:37:25,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:25,638] [INFO] Task started: Prodigal
[2024-01-24 12:37:25,639] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc7dcde3-4a59-43b8-8786-bb47b35f9487/GCF_011762095.1_ASM1176209v1_genomic.fna.gz | prodigal -d GCF_011762095.1_ASM1176209v1_genomic.fna/cds.fna -a GCF_011762095.1_ASM1176209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:37,232] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:37,232] [INFO] Task started: HMMsearch
[2024-01-24 12:37:37,233] [INFO] Running command: hmmsearch --tblout GCF_011762095.1_ASM1176209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference/reference_markers.hmm GCF_011762095.1_ASM1176209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:37,507] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:37,509] [INFO] Found 6/6 markers.
[2024-01-24 12:37:37,547] [INFO] Query marker FASTA was written to GCF_011762095.1_ASM1176209v1_genomic.fna/markers.fasta
[2024-01-24 12:37:37,547] [INFO] Task started: Blastn
[2024-01-24 12:37:37,547] [INFO] Running command: blastn -query GCF_011762095.1_ASM1176209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference/reference_markers.fasta -out GCF_011762095.1_ASM1176209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:38,560] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:38,564] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:38,564] [INFO] Target genome list was writen to GCF_011762095.1_ASM1176209v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:38,576] [INFO] Task started: fastANI
[2024-01-24 12:37:38,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc7dcde3-4a59-43b8-8786-bb47b35f9487/GCF_011762095.1_ASM1176209v1_genomic.fna.gz --refList GCF_011762095.1_ASM1176209v1_genomic.fna/target_genomes.txt --output GCF_011762095.1_ASM1176209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:54,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:54,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:54,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:54,450] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:54,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:54,451] [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
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	100.0	1322	1324	95	conclusive
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	79.1494	553	1324	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.0651	500	1324	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	78.2186	382	1324	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.5029	283	1324	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	77.4623	284	1324	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.9346	214	1324	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.8166	169	1324	95	below_threshold
Blastochloris viridis	strain=DSM 133	GCA_001548155.2	1079	1079	type	True	76.7987	153	1324	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	76.79	172	1324	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.7885	190	1324	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.7677	193	1324	95	below_threshold
Blastochloris viridis	strain=ATCC 19567	GCA_001402875.1	1079	1079	type	True	76.7377	154	1324	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	76.7034	168	1324	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.6405	173	1324	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.6324	144	1324	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.5795	177	1324	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	76.4475	181	1324	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.3159	136	1324	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1917	170	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,453] [INFO] DFAST Taxonomy check result was written to GCF_011762095.1_ASM1176209v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:54,454] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:54,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:54,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference/checkm_data
[2024-01-24 12:37:54,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:54,501] [INFO] Task started: CheckM
[2024-01-24 12:37:54,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011762095.1_ASM1176209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011762095.1_ASM1176209v1_genomic.fna/checkm_input GCF_011762095.1_ASM1176209v1_genomic.fna/checkm_result
[2024-01-24 12:38:31,093] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:31,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:31,113] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:31,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:31,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011762095.1_ASM1176209v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:31,115] [INFO] Task started: Blastn
[2024-01-24 12:38:31,115] [INFO] Running command: blastn -query GCF_011762095.1_ASM1176209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6935943-3a40-4de8-be81-935e7e702b85/dqc_reference/reference_markers_gtdb.fasta -out GCF_011762095.1_ASM1176209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:33,056] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:33,060] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:33,060] [INFO] Target genome list was writen to GCF_011762095.1_ASM1176209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:33,070] [INFO] Task started: fastANI
[2024-01-24 12:38:33,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc7dcde3-4a59-43b8-8786-bb47b35f9487/GCF_011762095.1_ASM1176209v1_genomic.fna.gz --refList GCF_011762095.1_ASM1176209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011762095.1_ASM1176209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:42,029] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:42,045] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:42,046] [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_011762095.1	s__Parvibaculum indicum	100.0	1322	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002684405.1	s__Parvibaculum sp002684405	90.5236	891	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694985.1	s__Parvibaculum sp002694985	80.1875	559	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002480495.1	s__Parvibaculum sp002480495	80.0557	592	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_002842875.1	s__Parvibaculum sp002842875	79.4897	522	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	79.3091	457	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	79.1249	556	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359855.1	s__Parvibaculum sp014359855	78.9328	338	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	78.8861	545	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_000751295.2	s__Phreatobacter sp000751295	77.0414	230	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	76.7803	192	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402875.1	s__Blastochloris viridis	76.7377	154	1324	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:42,048] [INFO] GTDB search result was written to GCF_011762095.1_ASM1176209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:42,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:42,053] [INFO] DFAST_QC result json was written to GCF_011762095.1_ASM1176209v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:42,054] [INFO] DFAST_QC completed!
[2024-01-24 12:38:42,054] [INFO] Total running time: 0h1m18s