[2023-06-16 19:08:45,047] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:08:45,050] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:08:45,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference
[2023-06-16 19:08:46,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:08:46,212] [INFO] Task started: Prodigal
[2023-06-16 19:08:46,212] [INFO] Running command: gunzip -c /var/lib/cwl/stg6577aa54-5f49-417f-a178-60978789b11f/GCA_028722065.1_ASM2872206v1_genomic.fna.gz | prodigal -d GCA_028722065.1_ASM2872206v1_genomic.fna/cds.fna -a GCA_028722065.1_ASM2872206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:08:51,324] [INFO] Task succeeded: Prodigal
[2023-06-16 19:08:51,324] [INFO] Task started: HMMsearch
[2023-06-16 19:08:51,324] [INFO] Running command: hmmsearch --tblout GCA_028722065.1_ASM2872206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference/reference_markers.hmm GCA_028722065.1_ASM2872206v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:08:51,498] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:08:51,499] [INFO] Found 6/6 markers.
[2023-06-16 19:08:51,518] [INFO] Query marker FASTA was written to GCA_028722065.1_ASM2872206v1_genomic.fna/markers.fasta
[2023-06-16 19:08:51,518] [INFO] Task started: Blastn
[2023-06-16 19:08:51,518] [INFO] Running command: blastn -query GCA_028722065.1_ASM2872206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference/reference_markers.fasta -out GCA_028722065.1_ASM2872206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:08:52,107] [INFO] Task succeeded: Blastn
[2023-06-16 19:08:52,111] [INFO] Selected 27 target genomes.
[2023-06-16 19:08:52,111] [INFO] Target genome list was writen to GCA_028722065.1_ASM2872206v1_genomic.fna/target_genomes.txt
[2023-06-16 19:08:52,140] [INFO] Task started: fastANI
[2023-06-16 19:08:52,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg6577aa54-5f49-417f-a178-60978789b11f/GCA_028722065.1_ASM2872206v1_genomic.fna.gz --refList GCA_028722065.1_ASM2872206v1_genomic.fna/target_genomes.txt --output GCA_028722065.1_ASM2872206v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:09:05,959] [INFO] Task succeeded: fastANI
[2023-06-16 19:09:05,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:09:05,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:09:05,962] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:09:05,962] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:09:05,962] [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
--------------------------------------------------------------------------------
[2023-06-16 19:09:05,963] [INFO] DFAST Taxonomy check result was written to GCA_028722065.1_ASM2872206v1_genomic.fna/tc_result.tsv
[2023-06-16 19:09:05,964] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:09:05,964] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:09:05,964] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference/checkm_data
[2023-06-16 19:09:05,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:09:05,988] [INFO] Task started: CheckM
[2023-06-16 19:09:05,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028722065.1_ASM2872206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028722065.1_ASM2872206v1_genomic.fna/checkm_input GCA_028722065.1_ASM2872206v1_genomic.fna/checkm_result
[2023-06-16 19:09:27,311] [INFO] Task succeeded: CheckM
[2023-06-16 19:09:27,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:09:27,333] [INFO] ===== Completeness check finished =====
[2023-06-16 19:09:27,333] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:09:27,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028722065.1_ASM2872206v1_genomic.fna/markers.fasta)
[2023-06-16 19:09:27,333] [INFO] Task started: Blastn
[2023-06-16 19:09:27,334] [INFO] Running command: blastn -query GCA_028722065.1_ASM2872206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd7b93ab-f4e2-4293-9351-12124ffb3566/dqc_reference/reference_markers_gtdb.fasta -out GCA_028722065.1_ASM2872206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:09:28,130] [INFO] Task succeeded: Blastn
[2023-06-16 19:09:28,135] [INFO] Selected 19 target genomes.
[2023-06-16 19:09:28,135] [INFO] Target genome list was writen to GCA_028722065.1_ASM2872206v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:09:28,171] [INFO] Task started: fastANI
[2023-06-16 19:09:28,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg6577aa54-5f49-417f-a178-60978789b11f/GCA_028722065.1_ASM2872206v1_genomic.fna.gz --refList GCA_028722065.1_ASM2872206v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028722065.1_ASM2872206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:09:35,053] [INFO] Task succeeded: fastANI
[2023-06-16 19:09:35,063] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:09:35,063] [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_000435055.1	s__PeH17 sp000435055	98.8659	567	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.45	98.03	0.92	0.89	15	conclusive
GCA_002309375.1	s__PeH17 sp002309375	78.2132	62	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001940845.1	s__PeH17 sp001940845	77.8429	56	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525875.1	s__PeH17 sp017525875	77.8422	77	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	97.79	97.79	0.91	0.91	2	-
GCA_902794055.1	s__PeH17 sp902794055	77.8236	86	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017395105.1	s__PeH17 sp017395105	77.7858	73	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542285.1	s__PeH17 sp900542285	77.7738	79	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.90	98.16	0.94	0.91	7	-
GCA_017538255.1	s__PeH17 sp017538255	77.4271	91	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288175.1	s__PeH17 sp016288175	77.3484	70	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	98.53	98.53	0.71	0.71	2	-
GCA_017523925.1	s__PeH17 sp017523925	77.2665	101	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282255.1	s__PeH17 sp016282255	77.157	56	600	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__PeH17	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:09:35,066] [INFO] GTDB search result was written to GCA_028722065.1_ASM2872206v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:09:35,066] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:09:35,069] [INFO] DFAST_QC result json was written to GCA_028722065.1_ASM2872206v1_genomic.fna/dqc_result.json
[2023-06-16 19:09:35,069] [INFO] DFAST_QC completed!
[2023-06-16 19:09:35,069] [INFO] Total running time: 0h0m50s