[2024-01-25 17:41:50,707] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:50,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:50,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference
[2024-01-25 17:41:51,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:51,847] [INFO] Task started: Prodigal
[2024-01-25 17:41:51,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ab709e9-4466-40ad-8494-c4d1c555f906/GCF_000429045.1_ASM42904v1_genomic.fna.gz | prodigal -d GCF_000429045.1_ASM42904v1_genomic.fna/cds.fna -a GCF_000429045.1_ASM42904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:03,545] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:03,545] [INFO] Task started: HMMsearch
[2024-01-25 17:42:03,545] [INFO] Running command: hmmsearch --tblout GCF_000429045.1_ASM42904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference/reference_markers.hmm GCF_000429045.1_ASM42904v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:03,841] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:03,842] [INFO] Found 6/6 markers.
[2024-01-25 17:42:03,884] [INFO] Query marker FASTA was written to GCF_000429045.1_ASM42904v1_genomic.fna/markers.fasta
[2024-01-25 17:42:03,884] [INFO] Task started: Blastn
[2024-01-25 17:42:03,884] [INFO] Running command: blastn -query GCF_000429045.1_ASM42904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference/reference_markers.fasta -out GCF_000429045.1_ASM42904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:04,997] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:05,000] [INFO] Selected 23 target genomes.
[2024-01-25 17:42:05,000] [INFO] Target genome list was writen to GCF_000429045.1_ASM42904v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:05,027] [INFO] Task started: fastANI
[2024-01-25 17:42:05,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab709e9-4466-40ad-8494-c4d1c555f906/GCF_000429045.1_ASM42904v1_genomic.fna.gz --refList GCF_000429045.1_ASM42904v1_genomic.fna/target_genomes.txt --output GCF_000429045.1_ASM42904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:30,978] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:30,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:30,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:30,992] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:30,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:30,992] [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
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	100.0	1711	1719	95	conclusive
Salinarimonas ramus	strain=CGMCC 1.9161	GCA_014645695.1	690164	690164	type	True	86.3781	1226	1719	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	79.216	702	1719	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.7743	634	1719	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	78.5373	665	1719	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	78.5274	724	1719	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	78.5143	738	1719	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	78.4554	519	1719	95	below_threshold
Chelatococcus composti	strain=CGMCC 1.15283	GCA_014641535.1	1743235	1743235	type	True	78.4135	508	1719	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_014201415.1	1743235	1743235	type	True	78.4092	494	1719	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	78.4076	499	1719	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	78.3668	504	1719	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	78.3549	523	1719	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	78.2869	662	1719	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	78.2772	683	1719	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	78.2659	616	1719	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	78.2047	595	1719	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	78.1679	642	1719	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	78.145	574	1719	95	below_threshold
Methylobacterium soli	strain=YIM 48816	GCA_008806385.1	553447	553447	type	True	78.0039	536	1719	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.9816	464	1719	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	77.9376	440	1719	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	77.6945	513	1719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:30,994] [INFO] DFAST Taxonomy check result was written to GCF_000429045.1_ASM42904v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:30,994] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:30,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:30,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference/checkm_data
[2024-01-25 17:42:30,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:31,045] [INFO] Task started: CheckM
[2024-01-25 17:42:31,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429045.1_ASM42904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429045.1_ASM42904v1_genomic.fna/checkm_input GCF_000429045.1_ASM42904v1_genomic.fna/checkm_result
[2024-01-25 17:43:26,216] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:26,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:26,237] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:26,237] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:26,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429045.1_ASM42904v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:26,238] [INFO] Task started: Blastn
[2024-01-25 17:43:26,238] [INFO] Running command: blastn -query GCF_000429045.1_ASM42904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg747cfca6-2f2d-4f06-8466-6721a0fac6fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429045.1_ASM42904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:28,713] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:28,716] [INFO] Selected 20 target genomes.
[2024-01-25 17:43:28,716] [INFO] Target genome list was writen to GCF_000429045.1_ASM42904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:28,746] [INFO] Task started: fastANI
[2024-01-25 17:43:28,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ab709e9-4466-40ad-8494-c4d1c555f906/GCF_000429045.1_ASM42904v1_genomic.fna.gz --refList GCF_000429045.1_ASM42904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429045.1_ASM42904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:53,636] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:53,648] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:53,648] [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_000429045.1	s__Salinarimonas rosea	100.0	1711	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014645695.1	s__Salinarimonas ramus	86.3585	1228	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386575.1	s__BN140002 sp008386575	79.1997	703	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__BN140002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693435.1	s__Salinarimonas sp007693435	79.1306	511	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	78.791	522	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196925.1	s__Chelatococcus_A caeni	78.7566	630	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_003173775.1	s__Methylobacterium sp003173775	78.5588	701	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_016613415.1	s__Methylobacterium ajmalii	78.5274	722	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	-
GCF_009363855.1	s__Microvirga thermotolerans	78.4436	522	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201415.1	s__Chelatococcus_A composti	78.3705	498	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.84	99.53	0.99	0.98	4	-
GCF_001713455.1	s__Bosea sp001713455	78.3475	583	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCF_001043955.1	s__Methylobacterium tarhaniae	78.2641	666	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173735.1	s__Methylobacterium radiodurans	78.2638	613	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351345.1	s__Bosea caraganae	78.2514	617	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011043735.1	s__Methylobacterium sp011043735	78.2272	727	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022085.1	s__Methylobacterium nodulans	78.2077	635	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141845.1	s__Methylobacterium symbioticum	78.1806	602	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019365.1	s__Methylobacterium sp000019365	78.1356	718	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_008806385.1	s__Methylobacterium soli	78.0003	536	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363955.1	s__Enterovirga rhinocerotis	77.6483	522	1719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Enterovirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:53,649] [INFO] GTDB search result was written to GCF_000429045.1_ASM42904v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:53,650] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:53,653] [INFO] DFAST_QC result json was written to GCF_000429045.1_ASM42904v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:53,654] [INFO] DFAST_QC completed!
[2024-01-25 17:43:53,654] [INFO] Total running time: 0h2m3s