[2023-06-13 13:52:22,375] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:52:22,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:52:22,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference
[2023-06-13 13:52:23,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:52:23,778] [INFO] Task started: Prodigal
[2023-06-13 13:52:23,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg674bee74-d3b9-464c-b1a5-9d096a6e8c71/GCA_022792845.1_ASM2279284v1_genomic.fna.gz | prodigal -d GCA_022792845.1_ASM2279284v1_genomic.fna/cds.fna -a GCA_022792845.1_ASM2279284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:52:28,748] [INFO] Task succeeded: Prodigal
[2023-06-13 13:52:28,749] [INFO] Task started: HMMsearch
[2023-06-13 13:52:28,749] [INFO] Running command: hmmsearch --tblout GCA_022792845.1_ASM2279284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference/reference_markers.hmm GCA_022792845.1_ASM2279284v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:52:28,964] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:52:28,967] [INFO] Found 6/6 markers.
[2023-06-13 13:52:28,993] [INFO] Query marker FASTA was written to GCA_022792845.1_ASM2279284v1_genomic.fna/markers.fasta
[2023-06-13 13:52:28,993] [INFO] Task started: Blastn
[2023-06-13 13:52:28,993] [INFO] Running command: blastn -query GCA_022792845.1_ASM2279284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference/reference_markers.fasta -out GCA_022792845.1_ASM2279284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:52:29,578] [INFO] Task succeeded: Blastn
[2023-06-13 13:52:29,583] [INFO] Selected 24 target genomes.
[2023-06-13 13:52:29,584] [INFO] Target genome list was writen to GCA_022792845.1_ASM2279284v1_genomic.fna/target_genomes.txt
[2023-06-13 13:52:29,603] [INFO] Task started: fastANI
[2023-06-13 13:52:29,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg674bee74-d3b9-464c-b1a5-9d096a6e8c71/GCA_022792845.1_ASM2279284v1_genomic.fna.gz --refList GCA_022792845.1_ASM2279284v1_genomic.fna/target_genomes.txt --output GCA_022792845.1_ASM2279284v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:52:43,019] [INFO] Task succeeded: fastANI
[2023-06-13 13:52:43,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:52:43,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:52:43,022] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:52:43,022] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:52:43,023] [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
--------------------------------------------------------------------------------
[2023-06-13 13:52:43,025] [INFO] DFAST Taxonomy check result was written to GCA_022792845.1_ASM2279284v1_genomic.fna/tc_result.tsv
[2023-06-13 13:52:43,026] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:52:43,027] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:52:43,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference/checkm_data
[2023-06-13 13:52:43,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:52:43,053] [INFO] Task started: CheckM
[2023-06-13 13:52:43,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022792845.1_ASM2279284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022792845.1_ASM2279284v1_genomic.fna/checkm_input GCA_022792845.1_ASM2279284v1_genomic.fna/checkm_result
[2023-06-13 13:53:04,277] [INFO] Task succeeded: CheckM
[2023-06-13 13:53:04,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:53:04,304] [INFO] ===== Completeness check finished =====
[2023-06-13 13:53:04,304] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:53:04,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022792845.1_ASM2279284v1_genomic.fna/markers.fasta)
[2023-06-13 13:53:04,305] [INFO] Task started: Blastn
[2023-06-13 13:53:04,305] [INFO] Running command: blastn -query GCA_022792845.1_ASM2279284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4979aee0-7f17-4e61-ac39-e1b15db550fe/dqc_reference/reference_markers_gtdb.fasta -out GCA_022792845.1_ASM2279284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:53:05,136] [INFO] Task succeeded: Blastn
[2023-06-13 13:53:05,142] [INFO] Selected 15 target genomes.
[2023-06-13 13:53:05,142] [INFO] Target genome list was writen to GCA_022792845.1_ASM2279284v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:53:05,144] [INFO] Task started: fastANI
[2023-06-13 13:53:05,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg674bee74-d3b9-464c-b1a5-9d096a6e8c71/GCA_022792845.1_ASM2279284v1_genomic.fna.gz --refList GCA_022792845.1_ASM2279284v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022792845.1_ASM2279284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:53:10,207] [INFO] Task succeeded: fastANI
[2023-06-13 13:53:10,224] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:53:10,224] [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_910586365.1	s__Gallimonas sp910586365	99.9244	567	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910589015.1	s__Gallimonas sp910589015	86.5884	502	611	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_910586245.1	s__Gallimonas sp910586245	78.8332	221	611	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_910586825.1	s__Gallimonas sp910586825	78.4738	184	611	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_904373325.1	s__Gallimonas merdigallinarum	78.1925	177	611	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	77.9536	130	611	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_910586675.1	s__Gallimonas sp910586675	77.9374	169	611	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_910586655.1	s__Gallimonas sp910586655	77.9007	119	611	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_910588695.1	s__Gallimonas sp910588695	77.8162	137	611	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_910586985.1	s__Gallimonas sp910586985	77.7682	109	611	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	77.2947	85	611	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	77.23	110	611	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_019117085.1	s__Gallimonas gallistercoris	77.0649	107	611	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_003343805.1	s__Gallimonas intestinavium	76.8284	98	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	96.93	96.83	0.81	0.77	3	-
GCA_900548845.1	s__Gallimonas sp900548845	76.8236	81	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	97.44	97.44	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-13 13:53:10,226] [INFO] GTDB search result was written to GCA_022792845.1_ASM2279284v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:53:10,227] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:53:10,230] [INFO] DFAST_QC result json was written to GCA_022792845.1_ASM2279284v1_genomic.fna/dqc_result.json
[2023-06-13 13:53:10,230] [INFO] DFAST_QC completed!
[2023-06-13 13:53:10,231] [INFO] Total running time: 0h0m48s