[2023-06-30 13:54:54,132] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:54:54,134] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:54:54,134] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference
[2023-06-30 13:54:56,168] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:54:56,169] [INFO] Task started: Prodigal
[2023-06-30 13:54:56,169] [INFO] Running command: gunzip -c /var/lib/cwl/stgc782cbae-c9c5-45b1-921c-e499a2e22934/GCA_019116755.1_ASM1911675v1_genomic.fna.gz | prodigal -d GCA_019116755.1_ASM1911675v1_genomic.fna/cds.fna -a GCA_019116755.1_ASM1911675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:55:01,059] [INFO] Task succeeded: Prodigal
[2023-06-30 13:55:01,059] [INFO] Task started: HMMsearch
[2023-06-30 13:55:01,060] [INFO] Running command: hmmsearch --tblout GCA_019116755.1_ASM1911675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference/reference_markers.hmm GCA_019116755.1_ASM1911675v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:55:01,299] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:55:01,301] [INFO] Found 6/6 markers.
[2023-06-30 13:55:01,329] [INFO] Query marker FASTA was written to GCA_019116755.1_ASM1911675v1_genomic.fna/markers.fasta
[2023-06-30 13:55:01,329] [INFO] Task started: Blastn
[2023-06-30 13:55:01,329] [INFO] Running command: blastn -query GCA_019116755.1_ASM1911675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference/reference_markers.fasta -out GCA_019116755.1_ASM1911675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:55:01,937] [INFO] Task succeeded: Blastn
[2023-06-30 13:55:01,942] [INFO] Selected 25 target genomes.
[2023-06-30 13:55:01,943] [INFO] Target genome list was writen to GCA_019116755.1_ASM1911675v1_genomic.fna/target_genomes.txt
[2023-06-30 13:55:01,949] [INFO] Task started: fastANI
[2023-06-30 13:55:01,950] [INFO] Running command: fastANI --query /var/lib/cwl/stgc782cbae-c9c5-45b1-921c-e499a2e22934/GCA_019116755.1_ASM1911675v1_genomic.fna.gz --refList GCA_019116755.1_ASM1911675v1_genomic.fna/target_genomes.txt --output GCA_019116755.1_ASM1911675v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:55:18,343] [INFO] Task succeeded: fastANI
[2023-06-30 13:55:18,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:55:18,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:55:18,346] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:55:18,347] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:55:18,347] [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
--------------------------------------------------------------------------------
[2023-06-30 13:55:18,349] [INFO] DFAST Taxonomy check result was written to GCA_019116755.1_ASM1911675v1_genomic.fna/tc_result.tsv
[2023-06-30 13:55:18,350] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:55:18,350] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:55:18,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference/checkm_data
[2023-06-30 13:55:18,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:55:18,379] [INFO] Task started: CheckM
[2023-06-30 13:55:18,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019116755.1_ASM1911675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019116755.1_ASM1911675v1_genomic.fna/checkm_input GCA_019116755.1_ASM1911675v1_genomic.fna/checkm_result
[2023-06-30 13:55:39,321] [INFO] Task succeeded: CheckM
[2023-06-30 13:55:39,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.44%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 13:55:39,344] [INFO] ===== Completeness check finished =====
[2023-06-30 13:55:39,345] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:55:39,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019116755.1_ASM1911675v1_genomic.fna/markers.fasta)
[2023-06-30 13:55:39,345] [INFO] Task started: Blastn
[2023-06-30 13:55:39,346] [INFO] Running command: blastn -query GCA_019116755.1_ASM1911675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4dd3c51-9709-4d60-b344-f13b8de656de/dqc_reference/reference_markers_gtdb.fasta -out GCA_019116755.1_ASM1911675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:55:40,232] [INFO] Task succeeded: Blastn
[2023-06-30 13:55:40,237] [INFO] Selected 14 target genomes.
[2023-06-30 13:55:40,238] [INFO] Target genome list was writen to GCA_019116755.1_ASM1911675v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:55:40,274] [INFO] Task started: fastANI
[2023-06-30 13:55:40,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgc782cbae-c9c5-45b1-921c-e499a2e22934/GCA_019116755.1_ASM1911675v1_genomic.fna.gz --refList GCA_019116755.1_ASM1911675v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019116755.1_ASM1911675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:55:44,575] [INFO] Task succeeded: fastANI
[2023-06-30 13:55:44,590] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:55:44,591] [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_003343805.1	s__Gallimonas intestinavium	97.0285	434	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	96.93	96.83	0.81	0.77	3	conclusive
GCA_900548845.1	s__Gallimonas sp900548845	88.8065	279	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	97.44	97.44	0.90	0.90	2	-
GCA_019117085.1	s__Gallimonas gallistercoris	88.7986	358	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116405.1	s__Gallimonas intestinigallinarum	79.4885	185	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904391375.1	s__Gallimonas faecavium	79.2655	173	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904419525.1	s__Gallimonas merdae	78.9864	164	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	99.30	98.70	0.95	0.93	3	-
GCF_904373325.1	s__Gallimonas merdigallinarum	78.8853	193	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.69	97.92	0.89	0.88	4	-
GCA_900547645.1	s__Gallimonas faecium	78.6647	152	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.43	98.37	0.87	0.83	4	-
GCA_900761685.1	s__Gallimonas intestinalis	78.4007	153	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	97.36	97.33	0.87	0.87	3	-
GCA_019114755.1	s__Borkfalkia faecavium	77.2934	109	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585235.1	s__Gallimonas sp910585235	77.1759	81	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804975.1	s__Gallimonas sp014804975	76.6603	54	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:55:44,593] [INFO] GTDB search result was written to GCA_019116755.1_ASM1911675v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:55:44,593] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:55:44,596] [INFO] DFAST_QC result json was written to GCA_019116755.1_ASM1911675v1_genomic.fna/dqc_result.json
[2023-06-30 13:55:44,596] [INFO] DFAST_QC completed!
[2023-06-30 13:55:44,596] [INFO] Total running time: 0h0m50s