[2023-06-30 13:54:24,312] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:54:24,315] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:54:24,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference
[2023-06-30 13:54:27,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:54:27,276] [INFO] Task started: Prodigal
[2023-06-30 13:54:27,277] [INFO] Running command: gunzip -c /var/lib/cwl/stg22093ab1-eac1-4b43-869f-4f592332f178/GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna.gz | prodigal -d GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/cds.fna -a GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:54:32,491] [INFO] Task succeeded: Prodigal
[2023-06-30 13:54:32,491] [INFO] Task started: HMMsearch
[2023-06-30 13:54:32,492] [INFO] Running command: hmmsearch --tblout GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference/reference_markers.hmm GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:54:32,698] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:54:32,699] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg22093ab1-eac1-4b43-869f-4f592332f178/GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna.gz]
[2023-06-30 13:54:32,720] [INFO] Query marker FASTA was written to GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/markers.fasta
[2023-06-30 13:54:32,721] [INFO] Task started: Blastn
[2023-06-30 13:54:32,721] [INFO] Running command: blastn -query GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/markers.fasta -db /var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference/reference_markers.fasta -out GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:54:33,306] [INFO] Task succeeded: Blastn
[2023-06-30 13:54:33,310] [INFO] Selected 17 target genomes.
[2023-06-30 13:54:33,310] [INFO] Target genome list was writen to GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/target_genomes.txt
[2023-06-30 13:54:33,315] [INFO] Task started: fastANI
[2023-06-30 13:54:33,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg22093ab1-eac1-4b43-869f-4f592332f178/GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna.gz --refList GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/target_genomes.txt --output GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:54:43,516] [INFO] Task succeeded: fastANI
[2023-06-30 13:54:43,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:54:43,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:54:43,528] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:54:43,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:54:43,528] [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 ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.783	89	175	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	78.2325	52	175	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.034	62	175	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	77.5607	58	175	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:54:43,531] [INFO] DFAST Taxonomy check result was written to GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/tc_result.tsv
[2023-06-30 13:54:43,531] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:54:43,532] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:54:43,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference/checkm_data
[2023-06-30 13:54:43,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:54:43,561] [INFO] Task started: CheckM
[2023-06-30 13:54:43,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/checkm_input GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/checkm_result
[2023-06-30 13:55:05,568] [INFO] Task succeeded: CheckM
[2023-06-30 13:55:05,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.18%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 13:55:05,594] [INFO] ===== Completeness check finished =====
[2023-06-30 13:55:05,594] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:55:05,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/markers.fasta)
[2023-06-30 13:55:05,595] [INFO] Task started: Blastn
[2023-06-30 13:55:05,596] [INFO] Running command: blastn -query GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/markers.fasta -db /var/lib/cwl/stg7367414f-ed66-4513-b84b-59e566028057/dqc_reference/reference_markers_gtdb.fasta -out GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:55:06,323] [INFO] Task succeeded: Blastn
[2023-06-30 13:55:06,328] [INFO] Selected 6 target genomes.
[2023-06-30 13:55:06,328] [INFO] Target genome list was writen to GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:55:06,353] [INFO] Task started: fastANI
[2023-06-30 13:55:06,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg22093ab1-eac1-4b43-869f-4f592332f178/GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna.gz --refList GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/target_genomes_gtdb.txt --output GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:55:09,998] [INFO] Task succeeded: fastANI
[2023-06-30 13:55:10,009] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:55:10,010] [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_903914175.1	s__Rhodoferax sp903914175	98.9868	162	175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.22	98.03	0.89	0.84	13	conclusive
GCA_903896425.1	s__Rhodoferax sp903896425	87.2245	120	175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.00	98.61	0.74	0.72	4	-
GCA_903876735.1	s__Rhodoferax sp903876735	84.7315	135	175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.69	99.51	0.95	0.90	9	-
GCA_903920695.1	s__Rhodoferax sp903920695	84.1412	130	175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.83	99.83	0.93	0.93	2	-
GCA_903828665.1	s__Rhodoferax sp903828665	84.1322	123	175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.74	99.58	0.91	0.86	28	-
GCA_016708345.1	s__Rhodoferax sp016708345	77.744	50	175	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.29	99.29	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-30 13:55:10,013] [INFO] GTDB search result was written to GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/result_gtdb.tsv
[2023-06-30 13:55:10,014] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:55:10,019] [INFO] DFAST_QC result json was written to GCA_903874935.1_freshwater_MAG_---_MJ120531B_bin-233_genomic.fna/dqc_result.json
[2023-06-30 13:55:10,020] [INFO] DFAST_QC completed!
[2023-06-30 13:55:10,020] [INFO] Total running time: 0h0m46s