[2024-01-24 14:11:46,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,691] [INFO] DQC Reference Directory: /var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference
[2024-01-24 14:11:47,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,927] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,927] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b6307ca-ab33-4f7f-876b-137c0a5438d7/GCF_003570715.1_ASM357071v1_genomic.fna.gz | prodigal -d GCF_003570715.1_ASM357071v1_genomic.fna/cds.fna -a GCF_003570715.1_ASM357071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:02,188] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:02,188] [INFO] Task started: HMMsearch
[2024-01-24 14:12:02,189] [INFO] Running command: hmmsearch --tblout GCF_003570715.1_ASM357071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference/reference_markers.hmm GCF_003570715.1_ASM357071v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:02,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:02,472] [INFO] Found 6/6 markers.
[2024-01-24 14:12:02,519] [INFO] Query marker FASTA was written to GCF_003570715.1_ASM357071v1_genomic.fna/markers.fasta
[2024-01-24 14:12:02,519] [INFO] Task started: Blastn
[2024-01-24 14:12:02,519] [INFO] Running command: blastn -query GCF_003570715.1_ASM357071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference/reference_markers.fasta -out GCF_003570715.1_ASM357071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:03,487] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:03,491] [INFO] Selected 13 target genomes.
[2024-01-24 14:12:03,491] [INFO] Target genome list was writen to GCF_003570715.1_ASM357071v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:03,503] [INFO] Task started: fastANI
[2024-01-24 14:12:03,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b6307ca-ab33-4f7f-876b-137c0a5438d7/GCF_003570715.1_ASM357071v1_genomic.fna.gz --refList GCF_003570715.1_ASM357071v1_genomic.fna/target_genomes.txt --output GCF_003570715.1_ASM357071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:16,168] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:16,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:16,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:16,180] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:16,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:16,181] [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
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	100.0	1521	1524	95	conclusive
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	91.4731	1181	1524	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	91.3513	1189	1524	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	83.5542	896	1524	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	82.2577	864	1524	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	81.6828	898	1524	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	81.3904	801	1524	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	81.3037	769	1524	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.9061	640	1524	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.8937	642	1524	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.5983	585	1524	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.4233	583	1524	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.8707	526	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:16,182] [INFO] DFAST Taxonomy check result was written to GCF_003570715.1_ASM357071v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:16,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:16,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:16,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference/checkm_data
[2024-01-24 14:12:16,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:16,231] [INFO] Task started: CheckM
[2024-01-24 14:12:16,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003570715.1_ASM357071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003570715.1_ASM357071v1_genomic.fna/checkm_input GCF_003570715.1_ASM357071v1_genomic.fna/checkm_result
[2024-01-24 14:13:06,434] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:06,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:06,458] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:06,459] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:06,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003570715.1_ASM357071v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:06,460] [INFO] Task started: Blastn
[2024-01-24 14:13:06,460] [INFO] Running command: blastn -query GCF_003570715.1_ASM357071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb59604ec-16fa-49a9-a1e5-46ee2c213344/dqc_reference/reference_markers_gtdb.fasta -out GCF_003570715.1_ASM357071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:08,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:08,221] [INFO] Selected 12 target genomes.
[2024-01-24 14:13:08,222] [INFO] Target genome list was writen to GCF_003570715.1_ASM357071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:08,258] [INFO] Task started: fastANI
[2024-01-24 14:13:08,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b6307ca-ab33-4f7f-876b-137c0a5438d7/GCF_003570715.1_ASM357071v1_genomic.fna.gz --refList GCF_003570715.1_ASM357071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003570715.1_ASM357071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:19,370] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:19,390] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:19,390] [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_003570715.1	s__Gemmobacter lutimaris	100.0	1521	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003054195.1	s__Gemmobacter caeni	91.4601	1183	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_008271655.1	s__Gemmobacter caeruleus	83.5357	899	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	82.2747	861	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	81.7849	659	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	81.3819	802	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973825.1	s__Gemmobacter serpentinus	81.3179	768	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003509785.1	s__Gemmobacter sp003509785	81.1093	653	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	99.39	99.26	0.82	0.79	4	-
GCF_007859075.1	s__Gemmobacter aquaticus	80.4615	673	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014859945.1	s__UBA1943 sp014859945	80.274	550	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336845.1	s__UBA1943 sp002336845	79.2697	565	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018058035.1	s__JAAKGP01 sp018058035	79.2302	546	1524	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:19,392] [INFO] GTDB search result was written to GCF_003570715.1_ASM357071v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:19,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:19,396] [INFO] DFAST_QC result json was written to GCF_003570715.1_ASM357071v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:19,396] [INFO] DFAST_QC completed!
[2024-01-24 14:13:19,396] [INFO] Total running time: 0h1m33s