[2024-01-24 13:40:44,086] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,088] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference
[2024-01-24 13:40:45,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,397] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg76520aa4-4aff-40ff-b773-1188f448ab39/GCF_002900965.1_ASM290096v1_genomic.fna.gz | prodigal -d GCF_002900965.1_ASM290096v1_genomic.fna/cds.fna -a GCF_002900965.1_ASM290096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,547] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,547] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,547] [INFO] Running command: hmmsearch --tblout GCF_002900965.1_ASM290096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference/reference_markers.hmm GCF_002900965.1_ASM290096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,810] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,845] [INFO] Query marker FASTA was written to GCF_002900965.1_ASM290096v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,846] [INFO] Task started: Blastn
[2024-01-24 13:40:58,846] [INFO] Running command: blastn -query GCF_002900965.1_ASM290096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference/reference_markers.fasta -out GCF_002900965.1_ASM290096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,880] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,884] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:59,885] [INFO] Target genome list was writen to GCF_002900965.1_ASM290096v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,890] [INFO] Task started: fastANI
[2024-01-24 13:40:59,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg76520aa4-4aff-40ff-b773-1188f448ab39/GCF_002900965.1_ASM290096v1_genomic.fna.gz --refList GCF_002900965.1_ASM290096v1_genomic.fna/target_genomes.txt --output GCF_002900965.1_ASM290096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:11,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:11,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:11,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:11,925] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:11,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:11,926] [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
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	88.1171	999	1225	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	85.2753	948	1225	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	83.2993	868	1225	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.7234	554	1225	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.6308	622	1225	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.238	538	1225	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.2246	540	1225	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	79.217	521	1225	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	79.1545	598	1225	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.0107	543	1225	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.9468	506	1225	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	78.8748	507	1225	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.793	493	1225	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	78.1962	412	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,928] [INFO] DFAST Taxonomy check result was written to GCF_002900965.1_ASM290096v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:11,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:11,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:11,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference/checkm_data
[2024-01-24 13:41:11,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:11,970] [INFO] Task started: CheckM
[2024-01-24 13:41:11,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002900965.1_ASM290096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002900965.1_ASM290096v1_genomic.fna/checkm_input GCF_002900965.1_ASM290096v1_genomic.fna/checkm_result
[2024-01-24 13:41:59,044] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:59,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,068] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:59,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:59,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002900965.1_ASM290096v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:59,069] [INFO] Task started: Blastn
[2024-01-24 13:41:59,069] [INFO] Running command: blastn -query GCF_002900965.1_ASM290096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a66396-9622-40e5-8e8f-c30075f5f00e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002900965.1_ASM290096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:00,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:00,849] [INFO] Selected 6 target genomes.
[2024-01-24 13:42:00,849] [INFO] Target genome list was writen to GCF_002900965.1_ASM290096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:00,866] [INFO] Task started: fastANI
[2024-01-24 13:42:00,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg76520aa4-4aff-40ff-b773-1188f448ab39/GCF_002900965.1_ASM290096v1_genomic.fna.gz --refList GCF_002900965.1_ASM290096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002900965.1_ASM290096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:06,599] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:06,609] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:06,610] [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_002900965.1	s__ETT8 sp002900965	100.0	1223	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004745575.1	s__ETT8 sp004745575	88.1171	999	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003443995.1	s__ETT8 sp003443995	85.2824	947	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	83.3068	867	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794355.1	s__ETT8 sp002794355	83.196	835	1225	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936395.1	s__ETT8 sp016936395	81.9475	649	1225	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 13:42:06,611] [INFO] GTDB search result was written to GCF_002900965.1_ASM290096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:06,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:06,615] [INFO] DFAST_QC result json was written to GCF_002900965.1_ASM290096v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:06,615] [INFO] DFAST_QC completed!
[2024-01-24 13:42:06,615] [INFO] Total running time: 0h1m23s