[2024-01-24 12:21:35,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:35,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:35,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference
[2024-01-24 12:21:37,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,178] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg7627d4de-f133-4000-8ce3-fc06d4279a3e/GCF_003121845.1_ASM312184v1_genomic.fna.gz | prodigal -d GCF_003121845.1_ASM312184v1_genomic.fna/cds.fna -a GCF_003121845.1_ASM312184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:42,142] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:42,142] [INFO] Task started: HMMsearch
[2024-01-24 12:21:42,142] [INFO] Running command: hmmsearch --tblout GCF_003121845.1_ASM312184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference/reference_markers.hmm GCF_003121845.1_ASM312184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:42,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:42,385] [INFO] Found 6/6 markers.
[2024-01-24 12:21:42,412] [INFO] Query marker FASTA was written to GCF_003121845.1_ASM312184v1_genomic.fna/markers.fasta
[2024-01-24 12:21:42,413] [INFO] Task started: Blastn
[2024-01-24 12:21:42,413] [INFO] Running command: blastn -query GCF_003121845.1_ASM312184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference/reference_markers.fasta -out GCF_003121845.1_ASM312184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:43,054] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:43,058] [INFO] Selected 18 target genomes.
[2024-01-24 12:21:43,059] [INFO] Target genome list was writen to GCF_003121845.1_ASM312184v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:43,283] [INFO] Task started: fastANI
[2024-01-24 12:21:43,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg7627d4de-f133-4000-8ce3-fc06d4279a3e/GCF_003121845.1_ASM312184v1_genomic.fna.gz --refList GCF_003121845.1_ASM312184v1_genomic.fna/target_genomes.txt --output GCF_003121845.1_ASM312184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:53,828] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:53,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:53,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:53,839] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:21:53,839] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:53,839] [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
Ignatzschineria ureiclastica	strain=KCTC 22644	GCA_003121845.1	472582	472582	type	True	100.0	800	801	95	conclusive
Ignatzschineria ureiclastica	strain=KCTC 22644	GCA_014652035.1	472582	472582	type	True	99.9912	790	801	95	conclusive
Ignatzschineria larvae	strain=DSM 13226	GCA_000510805.1	112009	112009	type	True	91.6789	656	801	95	below_threshold
Ignatzschineria indica	strain=KCTC 22643	GCA_003121925.1	472583	472583	type	True	78.9597	228	801	95	below_threshold
Ignatzschineria indica	strain=KCTC 22643	GCA_014652015.1	472583	472583	type	True	78.7979	227	801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:53,841] [INFO] DFAST Taxonomy check result was written to GCF_003121845.1_ASM312184v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:53,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:53,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:53,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference/checkm_data
[2024-01-24 12:21:53,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:53,872] [INFO] Task started: CheckM
[2024-01-24 12:21:53,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003121845.1_ASM312184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003121845.1_ASM312184v1_genomic.fna/checkm_input GCF_003121845.1_ASM312184v1_genomic.fna/checkm_result
[2024-01-24 12:22:15,820] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:15,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:15,845] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:15,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:15,846] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003121845.1_ASM312184v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:15,846] [INFO] Task started: Blastn
[2024-01-24 12:22:15,847] [INFO] Running command: blastn -query GCF_003121845.1_ASM312184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0116dfa3-1351-484f-98b6-ca50f22eca77/dqc_reference/reference_markers_gtdb.fasta -out GCF_003121845.1_ASM312184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:16,896] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:16,900] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:16,901] [INFO] Target genome list was writen to GCF_003121845.1_ASM312184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:16,954] [INFO] Task started: fastANI
[2024-01-24 12:22:16,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg7627d4de-f133-4000-8ce3-fc06d4279a3e/GCF_003121845.1_ASM312184v1_genomic.fna.gz --refList GCF_003121845.1_ASM312184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003121845.1_ASM312184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:24,864] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:24,878] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:24,879] [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_003121845.1	s__Ignatzschineria ureiclastica	100.0	800	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000510805.1	s__Ignatzschineria larvae	91.6964	655	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252045.1	s__Ignatzschineria sp002252045	79.0276	237	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121895.1	s__Ignatzschineria cameli	78.9726	205	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	99.12	98.86	0.95	0.93	5	-
GCF_003121925.1	s__Ignatzschineria indica	78.9597	228	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	99.99	99.99	1.00	1.00	2	-
GCA_019113305.1	s__Ignatzschineria merdigallinarum	78.1292	201	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__Ignatzschineria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513365.1	s__JAAZCI01 sp012513365	76.7774	71	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Wohlfahrtiimonadaceae;g__JAAZCI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:24,880] [INFO] GTDB search result was written to GCF_003121845.1_ASM312184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:24,881] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:24,883] [INFO] DFAST_QC result json was written to GCF_003121845.1_ASM312184v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:24,883] [INFO] DFAST_QC completed!
[2024-01-24 12:22:24,884] [INFO] Total running time: 0h0m49s