[2023-06-26 23:45:19,423] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:45:19,425] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:45:19,425] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference
[2023-06-26 23:45:20,667] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:45:20,668] [INFO] Task started: Prodigal
[2023-06-26 23:45:20,668] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ce8f053-7f31-42f6-b933-d8b8e8b5e752/GCA_026129085.1_ASM2612908v1_genomic.fna.gz | prodigal -d GCA_026129085.1_ASM2612908v1_genomic.fna/cds.fna -a GCA_026129085.1_ASM2612908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:45:41,754] [INFO] Task succeeded: Prodigal
[2023-06-26 23:45:41,755] [INFO] Task started: HMMsearch
[2023-06-26 23:45:41,755] [INFO] Running command: hmmsearch --tblout GCA_026129085.1_ASM2612908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference/reference_markers.hmm GCA_026129085.1_ASM2612908v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:45:42,121] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:45:42,123] [INFO] Found 6/6 markers.
[2023-06-26 23:45:42,201] [INFO] Query marker FASTA was written to GCA_026129085.1_ASM2612908v1_genomic.fna/markers.fasta
[2023-06-26 23:45:42,202] [INFO] Task started: Blastn
[2023-06-26 23:45:42,203] [INFO] Running command: blastn -query GCA_026129085.1_ASM2612908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference/reference_markers.fasta -out GCA_026129085.1_ASM2612908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:45:43,068] [INFO] Task succeeded: Blastn
[2023-06-26 23:45:43,074] [INFO] Selected 31 target genomes.
[2023-06-26 23:45:43,074] [INFO] Target genome list was writen to GCA_026129085.1_ASM2612908v1_genomic.fna/target_genomes.txt
[2023-06-26 23:45:43,093] [INFO] Task started: fastANI
[2023-06-26 23:45:43,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce8f053-7f31-42f6-b933-d8b8e8b5e752/GCA_026129085.1_ASM2612908v1_genomic.fna.gz --refList GCA_026129085.1_ASM2612908v1_genomic.fna/target_genomes.txt --output GCA_026129085.1_ASM2612908v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:46:00,282] [INFO] Task succeeded: fastANI
[2023-06-26 23:46:00,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:46:00,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:46:00,293] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:46:00,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:46:00,294] [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
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	74.9121	59	2412	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	74.8571	58	2412	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	74.8046	74	2412	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	74.7999	65	2412	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	74.7976	66	2412	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	74.7739	68	2412	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	74.769	69	2412	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	74.7483	60	2412	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	74.7299	77	2412	95	below_threshold
Deinococcus gobiensis	strain=I-0	GCA_000252445.1	502394	502394	type	True	74.6926	50	2412	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:46:00,296] [INFO] DFAST Taxonomy check result was written to GCA_026129085.1_ASM2612908v1_genomic.fna/tc_result.tsv
[2023-06-26 23:46:00,297] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:46:00,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:46:00,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference/checkm_data
[2023-06-26 23:46:00,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:46:00,378] [INFO] Task started: CheckM
[2023-06-26 23:46:00,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026129085.1_ASM2612908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026129085.1_ASM2612908v1_genomic.fna/checkm_input GCA_026129085.1_ASM2612908v1_genomic.fna/checkm_result
[2023-06-26 23:46:59,723] [INFO] Task succeeded: CheckM
[2023-06-26 23:46:59,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:46:59,755] [INFO] ===== Completeness check finished =====
[2023-06-26 23:46:59,755] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:46:59,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026129085.1_ASM2612908v1_genomic.fna/markers.fasta)
[2023-06-26 23:46:59,756] [INFO] Task started: Blastn
[2023-06-26 23:46:59,757] [INFO] Running command: blastn -query GCA_026129085.1_ASM2612908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd95d94b-5f18-4b83-ada6-aec3414bf323/dqc_reference/reference_markers_gtdb.fasta -out GCA_026129085.1_ASM2612908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:47:00,572] [INFO] Task succeeded: Blastn
[2023-06-26 23:47:00,578] [INFO] Selected 20 target genomes.
[2023-06-26 23:47:00,578] [INFO] Target genome list was writen to GCA_026129085.1_ASM2612908v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:47:00,604] [INFO] Task started: fastANI
[2023-06-26 23:47:00,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ce8f053-7f31-42f6-b933-d8b8e8b5e752/GCA_026129085.1_ASM2612908v1_genomic.fna.gz --refList GCA_026129085.1_ASM2612908v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026129085.1_ASM2612908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:47:13,999] [INFO] Task succeeded: fastANI
[2023-06-26 23:47:14,010] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:47:14,010] [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_017307785.1	s__JADMJV01 sp017307785	80.9703	1325	2412	d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__JADMJV01;g__JADMJV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266105.1	s__JADMJV01 sp018266105	78.8621	901	2412	d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__JADMJV01;g__JADMJV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780265.1	s__JADMJV01 sp018780265	77.469	458	2412	d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__JADMJV01;g__JADMJV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012799975.1	s__Xenobium sp012799975	75.5583	55	2412	d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__Xenobiaceae;g__Xenobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423485.1	s__Xenobium occultum	75.192	54	2412	d__Bacteria;p__Eremiobacterota;c__Xenobia;o__Xenobiales;f__Xenobiaceae;g__Xenobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868975.1	s__VGFD01 sp016868975	75.0547	73	2412	d__Bacteria;p__Eremiobacterota;c__Xenobia;o__RGZZ01;f__RGZZ01;g__VGFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143965.1	s__Desulfarculus baarsii	74.8993	60	2412	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Desulfarculus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842975.1	s__Rhodanobacter sp014842975	74.89	63	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307865.1	s__Ottowia sp017307865	74.8124	67	2412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ottowia	95.0	98.48	98.25	0.89	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-26 23:47:14,012] [INFO] GTDB search result was written to GCA_026129085.1_ASM2612908v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:47:14,013] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:47:14,016] [INFO] DFAST_QC result json was written to GCA_026129085.1_ASM2612908v1_genomic.fna/dqc_result.json
[2023-06-26 23:47:14,016] [INFO] DFAST_QC completed!
[2023-06-26 23:47:14,016] [INFO] Total running time: 0h1m55s