[2023-06-28 16:43:01,290] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:43:01,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:43:01,293] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference
[2023-06-28 16:43:02,600] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:43:02,601] [INFO] Task started: Prodigal
[2023-06-28 16:43:02,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg2233c87f-7216-4790-9434-8bbb2d1f999a/GCA_017404785.1_ASM1740478v1_genomic.fna.gz | prodigal -d GCA_017404785.1_ASM1740478v1_genomic.fna/cds.fna -a GCA_017404785.1_ASM1740478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:43:05,533] [INFO] Task succeeded: Prodigal
[2023-06-28 16:43:05,533] [INFO] Task started: HMMsearch
[2023-06-28 16:43:05,533] [INFO] Running command: hmmsearch --tblout GCA_017404785.1_ASM1740478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference/reference_markers.hmm GCA_017404785.1_ASM1740478v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:43:05,739] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:43:05,746] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2233c87f-7216-4790-9434-8bbb2d1f999a/GCA_017404785.1_ASM1740478v1_genomic.fna.gz]
[2023-06-28 16:43:05,770] [INFO] Query marker FASTA was written to GCA_017404785.1_ASM1740478v1_genomic.fna/markers.fasta
[2023-06-28 16:43:05,771] [INFO] Task started: Blastn
[2023-06-28 16:43:05,771] [INFO] Running command: blastn -query GCA_017404785.1_ASM1740478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference/reference_markers.fasta -out GCA_017404785.1_ASM1740478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:06,340] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:06,346] [INFO] Selected 17 target genomes.
[2023-06-28 16:43:06,346] [INFO] Target genome list was writen to GCA_017404785.1_ASM1740478v1_genomic.fna/target_genomes.txt
[2023-06-28 16:43:06,441] [INFO] Task started: fastANI
[2023-06-28 16:43:06,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg2233c87f-7216-4790-9434-8bbb2d1f999a/GCA_017404785.1_ASM1740478v1_genomic.fna.gz --refList GCA_017404785.1_ASM1740478v1_genomic.fna/target_genomes.txt --output GCA_017404785.1_ASM1740478v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:43:17,164] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:17,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:43:17,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:43:17,168] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:43:17,168] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:43:17,168] [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
--------------------------------------------------------------------------------
[2023-06-28 16:43:17,171] [INFO] DFAST Taxonomy check result was written to GCA_017404785.1_ASM1740478v1_genomic.fna/tc_result.tsv
[2023-06-28 16:43:17,172] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:43:17,172] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:43:17,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference/checkm_data
[2023-06-28 16:43:17,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:43:17,194] [INFO] Task started: CheckM
[2023-06-28 16:43:17,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017404785.1_ASM1740478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017404785.1_ASM1740478v1_genomic.fna/checkm_input GCA_017404785.1_ASM1740478v1_genomic.fna/checkm_result
[2023-06-28 16:43:34,941] [INFO] Task succeeded: CheckM
[2023-06-28 16:43:34,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:43:34,964] [INFO] ===== Completeness check finished =====
[2023-06-28 16:43:34,964] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:43:34,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017404785.1_ASM1740478v1_genomic.fna/markers.fasta)
[2023-06-28 16:43:34,965] [INFO] Task started: Blastn
[2023-06-28 16:43:34,965] [INFO] Running command: blastn -query GCA_017404785.1_ASM1740478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ec5b6f-099b-482f-bf16-50810305c944/dqc_reference/reference_markers_gtdb.fasta -out GCA_017404785.1_ASM1740478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:35,719] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:35,723] [INFO] Selected 13 target genomes.
[2023-06-28 16:43:35,723] [INFO] Target genome list was writen to GCA_017404785.1_ASM1740478v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:43:35,732] [INFO] Task started: fastANI
[2023-06-28 16:43:35,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg2233c87f-7216-4790-9434-8bbb2d1f999a/GCA_017404785.1_ASM1740478v1_genomic.fna.gz --refList GCA_017404785.1_ASM1740478v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017404785.1_ASM1740478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:43:40,307] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:40,323] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:43:40,324] [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_017404785.1	s__UBA636 sp017404785	100.0	421	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902803275.1	s__UBA636 sp902803275	82.4539	176	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	97.92	97.77	0.81	0.77	3	-
GCA_017511325.1	s__UBA636 sp017511325	82.4464	131	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550145.1	s__UBA636 sp017550145	79.3978	159	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428765.1	s__UBA636 sp017428765	79.1267	128	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	97.78	97.78	0.93	0.93	2	-
GCA_017432545.1	s__UBA636 sp017432545	78.8671	131	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017454765.1	s__UBA636 sp017454765	78.7571	129	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017539025.1	s__UBA636 sp017539025	78.6882	155	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432895.1	s__UBA636 sp017432895	78.5612	135	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017515475.1	s__UBA636 sp017515475	77.9101	90	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620435.1	s__UBA636 sp017620435	77.7856	97	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017431825.1	s__UBA636 sp017431825	77.0111	50	423	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__UBA636	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:43:40,326] [INFO] GTDB search result was written to GCA_017404785.1_ASM1740478v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:43:40,326] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:43:40,330] [INFO] DFAST_QC result json was written to GCA_017404785.1_ASM1740478v1_genomic.fna/dqc_result.json
[2023-06-28 16:43:40,330] [INFO] DFAST_QC completed!
[2023-06-28 16:43:40,330] [INFO] Total running time: 0h0m39s