[2023-06-13 15:27:36,740] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:27:36,746] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:27:36,746] [INFO] DQC Reference Directory: /var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference
[2023-06-13 15:27:38,181] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:27:38,182] [INFO] Task started: Prodigal
[2023-06-13 15:27:38,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg578569e8-2c74-4696-afda-8d6a79a4e72c/GCA_947449505.1_Jr-20nov17-78_genomic.fna.gz | prodigal -d GCA_947449505.1_Jr-20nov17-78_genomic.fna/cds.fna -a GCA_947449505.1_Jr-20nov17-78_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:27:43,353] [INFO] Task succeeded: Prodigal
[2023-06-13 15:27:43,354] [INFO] Task started: HMMsearch
[2023-06-13 15:27:43,354] [INFO] Running command: hmmsearch --tblout GCA_947449505.1_Jr-20nov17-78_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference/reference_markers.hmm GCA_947449505.1_Jr-20nov17-78_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:27:43,554] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:27:43,556] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg578569e8-2c74-4696-afda-8d6a79a4e72c/GCA_947449505.1_Jr-20nov17-78_genomic.fna.gz]
[2023-06-13 15:27:43,580] [INFO] Query marker FASTA was written to GCA_947449505.1_Jr-20nov17-78_genomic.fna/markers.fasta
[2023-06-13 15:27:43,580] [INFO] Task started: Blastn
[2023-06-13 15:27:43,581] [INFO] Running command: blastn -query GCA_947449505.1_Jr-20nov17-78_genomic.fna/markers.fasta -db /var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference/reference_markers.fasta -out GCA_947449505.1_Jr-20nov17-78_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:44,093] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:44,097] [INFO] Selected 10 target genomes.
[2023-06-13 15:27:44,097] [INFO] Target genome list was writen to GCA_947449505.1_Jr-20nov17-78_genomic.fna/target_genomes.txt
[2023-06-13 15:27:44,101] [INFO] Task started: fastANI
[2023-06-13 15:27:44,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg578569e8-2c74-4696-afda-8d6a79a4e72c/GCA_947449505.1_Jr-20nov17-78_genomic.fna.gz --refList GCA_947449505.1_Jr-20nov17-78_genomic.fna/target_genomes.txt --output GCA_947449505.1_Jr-20nov17-78_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:27:50,698] [INFO] Task succeeded: fastANI
[2023-06-13 15:27:50,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:27:50,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:27:50,714] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:27:50,714] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:27:50,714] [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=JCM 7819	GCA_002017865.1	28066	28066	type	True	78.1697	90	510	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	78.1045	91	510	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.6393	108	510	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	77.5553	105	510	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	77.4623	89	510	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.4596	91	510	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.4581	91	510	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.3748	112	510	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	76.9302	63	510	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:27:50,716] [INFO] DFAST Taxonomy check result was written to GCA_947449505.1_Jr-20nov17-78_genomic.fna/tc_result.tsv
[2023-06-13 15:27:50,717] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:27:50,717] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:27:50,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference/checkm_data
[2023-06-13 15:27:50,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:27:50,736] [INFO] Task started: CheckM
[2023-06-13 15:27:50,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947449505.1_Jr-20nov17-78_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947449505.1_Jr-20nov17-78_genomic.fna/checkm_input GCA_947449505.1_Jr-20nov17-78_genomic.fna/checkm_result
[2023-06-13 15:28:13,583] [INFO] Task succeeded: CheckM
[2023-06-13 15:28:13,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:28:13,609] [INFO] ===== Completeness check finished =====
[2023-06-13 15:28:13,610] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:28:13,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947449505.1_Jr-20nov17-78_genomic.fna/markers.fasta)
[2023-06-13 15:28:13,611] [INFO] Task started: Blastn
[2023-06-13 15:28:13,611] [INFO] Running command: blastn -query GCA_947449505.1_Jr-20nov17-78_genomic.fna/markers.fasta -db /var/lib/cwl/stga44cb2c9-b828-4610-ad21-c379645c7493/dqc_reference/reference_markers_gtdb.fasta -out GCA_947449505.1_Jr-20nov17-78_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:28:14,146] [INFO] Task succeeded: Blastn
[2023-06-13 15:28:14,150] [INFO] Selected 10 target genomes.
[2023-06-13 15:28:14,150] [INFO] Target genome list was writen to GCA_947449505.1_Jr-20nov17-78_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:28:14,153] [INFO] Task started: fastANI
[2023-06-13 15:28:14,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg578569e8-2c74-4696-afda-8d6a79a4e72c/GCA_947449505.1_Jr-20nov17-78_genomic.fna.gz --refList GCA_947449505.1_Jr-20nov17-78_genomic.fna/target_genomes_gtdb.txt --output GCA_947449505.1_Jr-20nov17-78_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:28:21,098] [INFO] Task succeeded: fastANI
[2023-06-13 15:28:21,117] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:28:21,117] [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_003347515.1	s__Rhodoferax sp003347515	79.3454	172	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840825.1	s__Rhodoferax sp903840825	79.3281	118	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780565.1	s__Rhodoferax sp018780565	78.6126	143	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795455.1	s__Rhodoferax sp001795455	78.1448	121	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.98	99.98	0.98	0.98	3	-
GCA_903886275.1	s__Rhodoferax sp903886275	77.9842	112	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.88	99.42	0.96	0.95	10	-
GCA_903920695.1	s__Rhodoferax sp903920695	77.8859	109	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903876735.1	s__Rhodoferax sp903876735	77.8826	126	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.69	99.51	0.95	0.90	9	-
GCA_903845935.1	s__Rhodoferax sp903845935	77.5619	112	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.58	99.41	0.92	0.88	22	-
GCA_009922295.1	s__Rhodoferax sp009922295	77.3492	70	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876045.1	s__Rhodoferax sp903876045	76.9946	80	510	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.28	99.14	0.84	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-13 15:28:21,120] [INFO] GTDB search result was written to GCA_947449505.1_Jr-20nov17-78_genomic.fna/result_gtdb.tsv
[2023-06-13 15:28:21,121] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:28:21,126] [INFO] DFAST_QC result json was written to GCA_947449505.1_Jr-20nov17-78_genomic.fna/dqc_result.json
[2023-06-13 15:28:21,126] [INFO] DFAST_QC completed!
[2023-06-13 15:28:21,126] [INFO] Total running time: 0h0m44s