[2024-01-24 12:06:24,400] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,404] [INFO] DQC Reference Directory: /var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference
[2024-01-24 12:06:25,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,814] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg733b2336-9ec9-4a7b-a143-6850d36863f4/GCF_014642635.1_ASM1464263v1_genomic.fna.gz | prodigal -d GCF_014642635.1_ASM1464263v1_genomic.fna/cds.fna -a GCF_014642635.1_ASM1464263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:39,464] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:39,464] [INFO] Task started: HMMsearch
[2024-01-24 12:06:39,464] [INFO] Running command: hmmsearch --tblout GCF_014642635.1_ASM1464263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference/reference_markers.hmm GCF_014642635.1_ASM1464263v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:39,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:39,763] [INFO] Found 6/6 markers.
[2024-01-24 12:06:39,814] [INFO] Query marker FASTA was written to GCF_014642635.1_ASM1464263v1_genomic.fna/markers.fasta
[2024-01-24 12:06:39,814] [INFO] Task started: Blastn
[2024-01-24 12:06:39,814] [INFO] Running command: blastn -query GCF_014642635.1_ASM1464263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference/reference_markers.fasta -out GCF_014642635.1_ASM1464263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:40,935] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:40,939] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:40,939] [INFO] Target genome list was writen to GCF_014642635.1_ASM1464263v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:40,946] [INFO] Task started: fastANI
[2024-01-24 12:06:40,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg733b2336-9ec9-4a7b-a143-6850d36863f4/GCF_014642635.1_ASM1464263v1_genomic.fna.gz --refList GCF_014642635.1_ASM1464263v1_genomic.fna/target_genomes.txt --output GCF_014642635.1_ASM1464263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:01,116] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:01,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:01,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:01,130] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:01,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:01,131] [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
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	100.0	1758	1759	95	conclusive
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	82.6629	992	1759	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	82.3734	921	1759	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	80.2711	780	1759	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	80.1261	728	1759	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	79.699	645	1759	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	79.5943	705	1759	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.5196	737	1759	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.4476	672	1759	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	79.3398	563	1759	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.9024	644	1759	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.6636	495	1759	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.6059	571	1759	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	78.5741	629	1759	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.4917	655	1759	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.9618	474	1759	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.9233	567	1759	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.9051	497	1759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:01,133] [INFO] DFAST Taxonomy check result was written to GCF_014642635.1_ASM1464263v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:01,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:01,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:01,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference/checkm_data
[2024-01-24 12:07:01,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:01,183] [INFO] Task started: CheckM
[2024-01-24 12:07:01,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642635.1_ASM1464263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642635.1_ASM1464263v1_genomic.fna/checkm_input GCF_014642635.1_ASM1464263v1_genomic.fna/checkm_result
[2024-01-24 12:07:42,895] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:42,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:42,916] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:42,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:42,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642635.1_ASM1464263v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:42,917] [INFO] Task started: Blastn
[2024-01-24 12:07:42,917] [INFO] Running command: blastn -query GCF_014642635.1_ASM1464263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea5e6c10-8be2-44be-ad37-f4ccd9d675c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642635.1_ASM1464263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,091] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,095] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:45,095] [INFO] Target genome list was writen to GCF_014642635.1_ASM1464263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:45,143] [INFO] Task started: fastANI
[2024-01-24 12:07:45,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg733b2336-9ec9-4a7b-a143-6850d36863f4/GCF_014642635.1_ASM1464263v1_genomic.fna.gz --refList GCF_014642635.1_ASM1464263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642635.1_ASM1464263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:00,258] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:00,269] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:00,270] [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_014642635.1	s__Aureimonas_A endophytica	100.0	1758	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009176975.1	s__Aureimonas_A psammosilene	82.7003	987	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	82.4009	917	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425485.1	s__Aureimonas_A sp001425485	80.9697	882	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001425575.1	s__Leaf443 sp001425575	80.8096	782	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424685.1	s__Aureimonas_A sp001424685	80.3543	790	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643375.1	s__Aureimonas_A glaciei	80.3516	813	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423245.1	s__Aureimonas sp001423245	80.3142	716	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442755.1	s__Aureimonas sp001442755	80.2956	818	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	98.47	96.94	0.96	0.92	3	-
GCF_003583935.1	s__Aureimonas flava	80.123	728	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893625.1	s__Mangrovicella endophytica	79.9698	668	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mangrovicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	79.4561	716	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014058705.1	s__Aureimonas mangrovi	79.369	560	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	79.244	693	1759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:00,271] [INFO] GTDB search result was written to GCF_014642635.1_ASM1464263v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:00,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:00,276] [INFO] DFAST_QC result json was written to GCF_014642635.1_ASM1464263v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:00,276] [INFO] DFAST_QC completed!
[2024-01-24 12:08:00,276] [INFO] Total running time: 0h1m36s