[2023-06-28 21:01:57,185] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:01:57,190] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:01:57,190] [INFO] DQC Reference Directory: /var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference
[2023-06-28 21:01:58,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:01:58,599] [INFO] Task started: Prodigal
[2023-06-28 21:01:58,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg085cea85-cfb3-41ae-bb3f-62687231720d/GCA_020048255.1_ASM2004825v1_genomic.fna.gz | prodigal -d GCA_020048255.1_ASM2004825v1_genomic.fna/cds.fna -a GCA_020048255.1_ASM2004825v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:02:06,333] [INFO] Task succeeded: Prodigal
[2023-06-28 21:02:06,334] [INFO] Task started: HMMsearch
[2023-06-28 21:02:06,334] [INFO] Running command: hmmsearch --tblout GCA_020048255.1_ASM2004825v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference/reference_markers.hmm GCA_020048255.1_ASM2004825v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:02:06,558] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:02:06,560] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg085cea85-cfb3-41ae-bb3f-62687231720d/GCA_020048255.1_ASM2004825v1_genomic.fna.gz]
[2023-06-28 21:02:06,598] [INFO] Query marker FASTA was written to GCA_020048255.1_ASM2004825v1_genomic.fna/markers.fasta
[2023-06-28 21:02:06,599] [INFO] Task started: Blastn
[2023-06-28 21:02:06,599] [INFO] Running command: blastn -query GCA_020048255.1_ASM2004825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference/reference_markers.fasta -out GCA_020048255.1_ASM2004825v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:07,260] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:07,264] [INFO] Selected 10 target genomes.
[2023-06-28 21:02:07,264] [INFO] Target genome list was writen to GCA_020048255.1_ASM2004825v1_genomic.fna/target_genomes.txt
[2023-06-28 21:02:07,265] [INFO] Task started: fastANI
[2023-06-28 21:02:07,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg085cea85-cfb3-41ae-bb3f-62687231720d/GCA_020048255.1_ASM2004825v1_genomic.fna.gz --refList GCA_020048255.1_ASM2004825v1_genomic.fna/target_genomes.txt --output GCA_020048255.1_ASM2004825v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:02:15,125] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:15,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:02:15,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:02:15,136] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:02:15,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:02:15,137] [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
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	79.1448	293	647	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	79.126	294	647	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	78.8997	271	647	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	78.825	273	647	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.2785	214	647	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.9246	195	647	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.452	151	647	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.4323	148	647	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	77.2965	140	647	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.2915	143	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:02:15,139] [INFO] DFAST Taxonomy check result was written to GCA_020048255.1_ASM2004825v1_genomic.fna/tc_result.tsv
[2023-06-28 21:02:15,140] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:02:15,140] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:02:15,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference/checkm_data
[2023-06-28 21:02:15,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:02:15,185] [INFO] Task started: CheckM
[2023-06-28 21:02:15,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020048255.1_ASM2004825v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020048255.1_ASM2004825v1_genomic.fna/checkm_input GCA_020048255.1_ASM2004825v1_genomic.fna/checkm_result
[2023-06-28 21:02:43,435] [INFO] Task succeeded: CheckM
[2023-06-28 21:02:43,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:02:43,460] [INFO] ===== Completeness check finished =====
[2023-06-28 21:02:43,460] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:02:43,461] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020048255.1_ASM2004825v1_genomic.fna/markers.fasta)
[2023-06-28 21:02:43,461] [INFO] Task started: Blastn
[2023-06-28 21:02:43,461] [INFO] Running command: blastn -query GCA_020048255.1_ASM2004825v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge83dea17-41a8-4d66-b716-406eb1d8f81e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020048255.1_ASM2004825v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:02:44,196] [INFO] Task succeeded: Blastn
[2023-06-28 21:02:44,201] [INFO] Selected 13 target genomes.
[2023-06-28 21:02:44,201] [INFO] Target genome list was writen to GCA_020048255.1_ASM2004825v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:02:44,205] [INFO] Task started: fastANI
[2023-06-28 21:02:44,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg085cea85-cfb3-41ae-bb3f-62687231720d/GCA_020048255.1_ASM2004825v1_genomic.fna.gz --refList GCA_020048255.1_ASM2004825v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020048255.1_ASM2004825v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:02:53,023] [INFO] Task succeeded: fastANI
[2023-06-28 21:02:53,042] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:02:53,042] [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
GCA_002083775.1	s__Rhodoferax ferrireducens_A	79.7823	348	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416775.1	s__Rhodoferax sp013416775	79.5308	287	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719055.1	s__Rhodoferax sp016719055	79.4944	302	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905735.1	s__Rhodoferax sp903905735	79.4303	313	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842265.1	s__Rhodoferax sp002842265	79.1924	227	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018619435.1	s__Rhodoferax sp018619435	79.1157	279	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002017865.1	s__Rhodoferax fermentans	79.1106	295	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001771065.1	s__Rhodoferax sp001771065	79.0813	249	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001871515.1	s__Rhodoferax sp001871515	78.9068	210	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.47	99.26	0.89	0.81	6	-
GCA_011391545.1	s__Rhodoferax sp011391545	78.8643	209	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001938565.1	s__Rhodoferax antarcticus	78.809	274	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903856025.1	s__Rhodoferax sp903856025	77.94	181	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.78	99.78	0.90	0.90	2	-
GCF_004341365.1	s__Giesbergeria metamorpha	77.2965	140	647	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-28 21:02:53,044] [INFO] GTDB search result was written to GCA_020048255.1_ASM2004825v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:02:53,045] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:02:53,050] [INFO] DFAST_QC result json was written to GCA_020048255.1_ASM2004825v1_genomic.fna/dqc_result.json
[2023-06-28 21:02:53,050] [INFO] DFAST_QC completed!
[2023-06-28 21:02:53,050] [INFO] Total running time: 0h0m56s