[2023-06-30 04:02:45,423] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:02:45,425] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:02:45,425] [INFO] DQC Reference Directory: /var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference
[2023-06-30 04:02:46,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:02:46,629] [INFO] Task started: Prodigal
[2023-06-30 04:02:46,629] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeb16531-e4b1-407c-ab57-4ecd13e456c4/GCA_016708155.1_ASM1670815v1_genomic.fna.gz | prodigal -d GCA_016708155.1_ASM1670815v1_genomic.fna/cds.fna -a GCA_016708155.1_ASM1670815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:02:56,711] [INFO] Task succeeded: Prodigal
[2023-06-30 04:02:56,712] [INFO] Task started: HMMsearch
[2023-06-30 04:02:56,712] [INFO] Running command: hmmsearch --tblout GCA_016708155.1_ASM1670815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference/reference_markers.hmm GCA_016708155.1_ASM1670815v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:02:56,932] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:02:56,934] [INFO] Found 6/6 markers.
[2023-06-30 04:02:56,966] [INFO] Query marker FASTA was written to GCA_016708155.1_ASM1670815v1_genomic.fna/markers.fasta
[2023-06-30 04:02:56,967] [INFO] Task started: Blastn
[2023-06-30 04:02:56,967] [INFO] Running command: blastn -query GCA_016708155.1_ASM1670815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference/reference_markers.fasta -out GCA_016708155.1_ASM1670815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:02:57,567] [INFO] Task succeeded: Blastn
[2023-06-30 04:02:57,573] [INFO] Selected 17 target genomes.
[2023-06-30 04:02:57,573] [INFO] Target genome list was writen to GCA_016708155.1_ASM1670815v1_genomic.fna/target_genomes.txt
[2023-06-30 04:02:57,577] [INFO] Task started: fastANI
[2023-06-30 04:02:57,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb16531-e4b1-407c-ab57-4ecd13e456c4/GCA_016708155.1_ASM1670815v1_genomic.fna.gz --refList GCA_016708155.1_ASM1670815v1_genomic.fna/target_genomes.txt --output GCA_016708155.1_ASM1670815v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:03:10,885] [INFO] Task succeeded: fastANI
[2023-06-30 04:03:10,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:03:10,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:03:10,892] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:03:10,892] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 04:03:10,892] [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
Tepidiforma bonchosmolovskayae	strain=3753O	GCA_008838325.1	2601677	2601677	type	True	77.7902	254	1140	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:03:10,895] [INFO] DFAST Taxonomy check result was written to GCA_016708155.1_ASM1670815v1_genomic.fna/tc_result.tsv
[2023-06-30 04:03:10,895] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:03:10,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:03:10,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference/checkm_data
[2023-06-30 04:03:10,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:03:10,941] [INFO] Task started: CheckM
[2023-06-30 04:03:10,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708155.1_ASM1670815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708155.1_ASM1670815v1_genomic.fna/checkm_input GCA_016708155.1_ASM1670815v1_genomic.fna/checkm_result
[2023-06-30 04:03:43,192] [INFO] Task succeeded: CheckM
[2023-06-30 04:03:43,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:03:43,216] [INFO] ===== Completeness check finished =====
[2023-06-30 04:03:43,216] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:03:43,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708155.1_ASM1670815v1_genomic.fna/markers.fasta)
[2023-06-30 04:03:43,217] [INFO] Task started: Blastn
[2023-06-30 04:03:43,217] [INFO] Running command: blastn -query GCA_016708155.1_ASM1670815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc72f93d5-ddc0-4b5f-9fce-f078b472b441/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708155.1_ASM1670815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:03:44,030] [INFO] Task succeeded: Blastn
[2023-06-30 04:03:44,035] [INFO] Selected 12 target genomes.
[2023-06-30 04:03:44,035] [INFO] Target genome list was writen to GCA_016708155.1_ASM1670815v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:03:44,037] [INFO] Task started: fastANI
[2023-06-30 04:03:44,038] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeb16531-e4b1-407c-ab57-4ecd13e456c4/GCA_016708155.1_ASM1670815v1_genomic.fna.gz --refList GCA_016708155.1_ASM1670815v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708155.1_ASM1670815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:03:51,352] [INFO] Task succeeded: fastANI
[2023-06-30 04:03:51,361] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:03:51,362] [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_016719395.1	s__FeB-14 sp016719395	98.5226	1059	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	98.39	98.17	0.95	0.93	9	conclusive
GCA_011055725.1	s__FeB-14 sp011055725	78.613	334	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003104995.1	s__FeB-14 sp003104995	78.1775	333	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__FeB-14	95.0	99.84	99.84	0.86	0.86	2	-
GCA_016703545.1	s__JACPOQ01 sp016703545	77.8256	251	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACPOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008838325.1	s__Tepidiforma bonchosmolovskayae	77.7592	255	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002563855.1	s__Tepidiforma sp002563855	77.7489	240	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__Tepidiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234445.1	s__JACRBT01 sp016234445	77.6636	288	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__JACRBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577245.1	s__UCB2 sp003577245	77.3579	123	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	99.02	98.75	0.69	0.69	3	-
GCA_015075555.1	s__UCB2 sp015075555	77.1088	203	1140	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Tepidiformales;f__Tepidiformaceae;g__UCB2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:03:51,364] [INFO] GTDB search result was written to GCA_016708155.1_ASM1670815v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:03:51,365] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:03:51,368] [INFO] DFAST_QC result json was written to GCA_016708155.1_ASM1670815v1_genomic.fna/dqc_result.json
[2023-06-30 04:03:51,368] [INFO] DFAST_QC completed!
[2023-06-30 04:03:51,368] [INFO] Total running time: 0h1m6s