[2024-01-25 19:12:20,423] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:20,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:20,425] [INFO] DQC Reference Directory: /var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference
[2024-01-25 19:12:21,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:21,602] [INFO] Task started: Prodigal
[2024-01-25 19:12:21,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgb247094c-9362-42bc-83fa-07baca8716d5/GCF_020165855.1_ASM2016585v1_genomic.fna.gz | prodigal -d GCF_020165855.1_ASM2016585v1_genomic.fna/cds.fna -a GCF_020165855.1_ASM2016585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:31,582] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:31,583] [INFO] Task started: HMMsearch
[2024-01-25 19:12:31,583] [INFO] Running command: hmmsearch --tblout GCF_020165855.1_ASM2016585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference/reference_markers.hmm GCF_020165855.1_ASM2016585v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:31,799] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:31,800] [INFO] Found 6/6 markers.
[2024-01-25 19:12:31,833] [INFO] Query marker FASTA was written to GCF_020165855.1_ASM2016585v1_genomic.fna/markers.fasta
[2024-01-25 19:12:31,833] [INFO] Task started: Blastn
[2024-01-25 19:12:31,833] [INFO] Running command: blastn -query GCF_020165855.1_ASM2016585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference/reference_markers.fasta -out GCF_020165855.1_ASM2016585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:32,500] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:32,505] [INFO] Selected 18 target genomes.
[2024-01-25 19:12:32,505] [INFO] Target genome list was writen to GCF_020165855.1_ASM2016585v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:32,521] [INFO] Task started: fastANI
[2024-01-25 19:12:32,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgb247094c-9362-42bc-83fa-07baca8716d5/GCF_020165855.1_ASM2016585v1_genomic.fna.gz --refList GCF_020165855.1_ASM2016585v1_genomic.fna/target_genomes.txt --output GCF_020165855.1_ASM2016585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:44,444] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:44,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:44,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:44,456] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:44,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:44,456] [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
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	100.0	1209	1209	95	conclusive
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	79.95	582	1209	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	79.7023	588	1209	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	79.5338	542	1209	95	below_threshold
Celeribacter halophilus	strain=DSM 26270	GCA_003254175.1	576117	576117	type	True	79.4596	478	1209	95	below_threshold
Celeribacter halophilus	strain=CGMCC 1.8891	GCA_900114135.1	576117	576117	type	True	79.4192	478	1209	95	below_threshold
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	79.3951	485	1209	95	below_threshold
Celeribacter indicus	strain=P73	GCA_900106965.1	1208324	1208324	type	True	78.3944	438	1209	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	78.3669	442	1209	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.6207	251	1209	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	76.926	143	1209	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.9012	145	1209	95	below_threshold
Pacificibacter marinus	strain=DSM 25228	GCA_900109555.1	658057	658057	type	True	76.8913	144	1209	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4551	139	1209	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.3964	168	1209	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.3803	149	1209	95	below_threshold
Paracoccus amoyensis	strain=11-3	GCA_014490725.1	2760093	2760093	type	True	76.325	85	1209	95	below_threshold
Paracoccus bogoriensis	strain=BOG6	GCA_019431455.1	242065	242065	type	True	75.8908	113	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:44,457] [INFO] DFAST Taxonomy check result was written to GCF_020165855.1_ASM2016585v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:44,458] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:44,458] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:44,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference/checkm_data
[2024-01-25 19:12:44,459] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:44,497] [INFO] Task started: CheckM
[2024-01-25 19:12:44,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020165855.1_ASM2016585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020165855.1_ASM2016585v1_genomic.fna/checkm_input GCF_020165855.1_ASM2016585v1_genomic.fna/checkm_result
[2024-01-25 19:13:16,338] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:16,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:16,357] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:16,357] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:16,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020165855.1_ASM2016585v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:16,357] [INFO] Task started: Blastn
[2024-01-25 19:13:16,357] [INFO] Running command: blastn -query GCF_020165855.1_ASM2016585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb44d1e19-1202-4ace-bed5-b20f6cd19022/dqc_reference/reference_markers_gtdb.fasta -out GCF_020165855.1_ASM2016585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:17,355] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:17,358] [INFO] Selected 12 target genomes.
[2024-01-25 19:13:17,358] [INFO] Target genome list was writen to GCF_020165855.1_ASM2016585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:17,389] [INFO] Task started: fastANI
[2024-01-25 19:13:17,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgb247094c-9362-42bc-83fa-07baca8716d5/GCF_020165855.1_ASM2016585v1_genomic.fna.gz --refList GCF_020165855.1_ASM2016585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020165855.1_ASM2016585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:26,331] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:26,339] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:13:26,339] [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_011806455.1	s__Celeribacter sp011806455	80.0784	548	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_001550095.1	s__Celeribacter ethanolicus	79.9406	583	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900113955.1	s__Celeribacter neptunius	79.7023	588	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050785.1	s__Celeribacter persicus	79.5338	542	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114135.1	s__Celeribacter halophilus	79.4092	479	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	-
GCF_000819565.1	s__Celeribacter indicus	78.3573	441	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.9012	145	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900109555.1	s__Pacificibacter marinus	76.8913	145	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002196855.1	s__Haematobacter sp002196855	76.7941	118	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Haematobacter	95.0	98.61	98.61	0.86	0.86	2	-
GCA_003428585.1	s__Nioella sp003428585	76.3898	140	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	76.3511	125	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490725.1	s__Paracoccus amoyensis	76.325	85	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:26,340] [INFO] GTDB search result was written to GCF_020165855.1_ASM2016585v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:26,341] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:26,344] [INFO] DFAST_QC result json was written to GCF_020165855.1_ASM2016585v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:26,344] [INFO] DFAST_QC completed!
[2024-01-25 19:13:26,344] [INFO] Total running time: 0h1m6s