[2024-01-24 12:40:08,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:08,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:08,086] [INFO] DQC Reference Directory: /var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference
[2024-01-24 12:40:09,444] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:09,445] [INFO] Task started: Prodigal
[2024-01-24 12:40:09,445] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ca63b9e-013f-42b3-84ee-c387b0f419fa/GCF_011059185.1_ASM1105918v1_genomic.fna.gz | prodigal -d GCF_011059185.1_ASM1105918v1_genomic.fna/cds.fna -a GCF_011059185.1_ASM1105918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:22,955] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:22,955] [INFO] Task started: HMMsearch
[2024-01-24 12:40:22,955] [INFO] Running command: hmmsearch --tblout GCF_011059185.1_ASM1105918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference/reference_markers.hmm GCF_011059185.1_ASM1105918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:23,233] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:23,235] [INFO] Found 6/6 markers.
[2024-01-24 12:40:23,281] [INFO] Query marker FASTA was written to GCF_011059185.1_ASM1105918v1_genomic.fna/markers.fasta
[2024-01-24 12:40:23,282] [INFO] Task started: Blastn
[2024-01-24 12:40:23,282] [INFO] Running command: blastn -query GCF_011059185.1_ASM1105918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference/reference_markers.fasta -out GCF_011059185.1_ASM1105918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:24,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:24,316] [INFO] Selected 15 target genomes.
[2024-01-24 12:40:24,316] [INFO] Target genome list was writen to GCF_011059185.1_ASM1105918v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:24,323] [INFO] Task started: fastANI
[2024-01-24 12:40:24,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca63b9e-013f-42b3-84ee-c387b0f419fa/GCF_011059185.1_ASM1105918v1_genomic.fna.gz --refList GCF_011059185.1_ASM1105918v1_genomic.fna/target_genomes.txt --output GCF_011059185.1_ASM1105918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:37,832] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:37,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:37,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:37,845] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:37,846] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:37,846] [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 ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	85.9898	995	1432	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	85.701	939	1432	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	85.7004	939	1432	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	81.4514	798	1432	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	80.6502	677	1432	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	80.2191	661	1432	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	80.1857	697	1432	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	80.0336	701	1432	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.8355	644	1432	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.7862	606	1432	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.7176	546	1432	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.6022	666	1432	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	79.1551	534	1432	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	78.5911	492	1432	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	78.5793	512	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:37,848] [INFO] DFAST Taxonomy check result was written to GCF_011059185.1_ASM1105918v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:37,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:37,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:37,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference/checkm_data
[2024-01-24 12:40:37,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:37,899] [INFO] Task started: CheckM
[2024-01-24 12:40:37,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011059185.1_ASM1105918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011059185.1_ASM1105918v1_genomic.fna/checkm_input GCF_011059185.1_ASM1105918v1_genomic.fna/checkm_result
[2024-01-24 12:41:25,123] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:25,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:25,144] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:25,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:25,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011059185.1_ASM1105918v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:25,146] [INFO] Task started: Blastn
[2024-01-24 12:41:25,146] [INFO] Running command: blastn -query GCF_011059185.1_ASM1105918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0cffc4a-eea9-4184-9225-4e274313a6c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_011059185.1_ASM1105918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:26,924] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:26,928] [INFO] Selected 8 target genomes.
[2024-01-24 12:41:26,928] [INFO] Target genome list was writen to GCF_011059185.1_ASM1105918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:26,934] [INFO] Task started: fastANI
[2024-01-24 12:41:26,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca63b9e-013f-42b3-84ee-c387b0f419fa/GCF_011059185.1_ASM1105918v1_genomic.fna.gz --refList GCF_011059185.1_ASM1105918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011059185.1_ASM1105918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:34,822] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:34,837] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:34,838] [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_011059185.1	s__Gemmobacter_B sp011059185	100.0	1426	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002855575.1	s__Gemmobacter_B sp002855575	86.1241	1009	1432	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_009908315.1	s__Gemmobacter_B sp009908315	85.9898	995	1432	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_009908265.2	s__Gemmobacter_B sp009908265	85.6659	942	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014654775.1	s__Gemmobacter_B sp014654775	85.2314	955	1432	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_000500915.1	s__Gemmobacter_B sp000500915	85.11	809	1432	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_013824045.1	s__Gemmobacter_B sp013824045	84.9777	638	1432	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_008271655.1	s__Gemmobacter caeruleus	80.6627	676	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:34,839] [INFO] GTDB search result was written to GCF_011059185.1_ASM1105918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:34,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:34,843] [INFO] DFAST_QC result json was written to GCF_011059185.1_ASM1105918v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:34,843] [INFO] DFAST_QC completed!
[2024-01-24 12:41:34,843] [INFO] Total running time: 0h1m27s