[2024-01-24 11:51:11,289] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,291] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,291] [INFO] DQC Reference Directory: /var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference
[2024-01-24 11:51:12,714] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,715] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,715] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeb5e8bc-ba52-4f39-814a-d7199fb6515a/GCF_017921895.1_ASM1792189v1_genomic.fna.gz | prodigal -d GCF_017921895.1_ASM1792189v1_genomic.fna/cds.fna -a GCF_017921895.1_ASM1792189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:33,131] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:33,131] [INFO] Task started: HMMsearch
[2024-01-24 11:51:33,131] [INFO] Running command: hmmsearch --tblout GCF_017921895.1_ASM1792189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference/reference_markers.hmm GCF_017921895.1_ASM1792189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:33,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:33,405] [INFO] Found 6/6 markers.
[2024-01-24 11:51:33,437] [INFO] Query marker FASTA was written to GCF_017921895.1_ASM1792189v1_genomic.fna/markers.fasta
[2024-01-24 11:51:33,438] [INFO] Task started: Blastn
[2024-01-24 11:51:33,438] [INFO] Running command: blastn -query GCF_017921895.1_ASM1792189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference/reference_markers.fasta -out GCF_017921895.1_ASM1792189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:34,062] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:34,069] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:34,070] [INFO] Target genome list was writen to GCF_017921895.1_ASM1792189v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:34,078] [INFO] Task started: fastANI
[2024-01-24 11:51:34,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb5e8bc-ba52-4f39-814a-d7199fb6515a/GCF_017921895.1_ASM1792189v1_genomic.fna.gz --refList GCF_017921895.1_ASM1792189v1_genomic.fna/target_genomes.txt --output GCF_017921895.1_ASM1792189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:47,703] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:47,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:47,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:47,708] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:47,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:47,708] [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
Natronogracilivirgula saccharolytica	strain=Z-1702	GCA_017921895.1	2812953	2812953	type	True	100.0	1226	1228	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:51:47,710] [INFO] DFAST Taxonomy check result was written to GCF_017921895.1_ASM1792189v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:47,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:47,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:47,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference/checkm_data
[2024-01-24 11:51:47,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:47,754] [INFO] Task started: CheckM
[2024-01-24 11:51:47,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017921895.1_ASM1792189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017921895.1_ASM1792189v1_genomic.fna/checkm_input GCF_017921895.1_ASM1792189v1_genomic.fna/checkm_result
[2024-01-24 11:52:47,505] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:47,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:47,526] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:47,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:47,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017921895.1_ASM1792189v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:47,526] [INFO] Task started: Blastn
[2024-01-24 11:52:47,526] [INFO] Running command: blastn -query GCF_017921895.1_ASM1792189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge190e952-98c3-4ae5-a5e2-cf01243084e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_017921895.1_ASM1792189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:48,321] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:48,326] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:48,326] [INFO] Target genome list was writen to GCF_017921895.1_ASM1792189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:48,339] [INFO] Task started: fastANI
[2024-01-24 11:52:48,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb5e8bc-ba52-4f39-814a-d7199fb6515a/GCF_017921895.1_ASM1792189v1_genomic.fna.gz --refList GCF_017921895.1_ASM1792189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017921895.1_ASM1792189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:55,406] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:55,416] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:55,416] [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_017921895.1	s__Natronogracilivirgula saccharolytica	100.0	1226	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__Natronogracilivirgula	95.0	99.72	99.69	0.98	0.97	5	conclusive
GCA_007134845.1	s__SKNL01 sp007134845	76.9428	98	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120555.1	s__SKNL01 sp007120555	76.8718	56	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	99.42	99.42	0.96	0.96	2	-
GCA_007693825.1	s__SKNL01 sp007693825	76.837	131	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133875.1	s__SLLW01 sp007133875	76.8239	104	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SLLW01	95.0	97.91	97.91	0.77	0.77	2	-
GCA_007127665.1	s__SKNL01 sp007127665	76.731	59	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	98.92	98.92	0.84	0.84	2	-
GCA_007132975.1	s__SKNL01 sp007132975	76.7109	121	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	99.80	99.78	0.93	0.93	3	-
GCA_007128425.1	s__SKNL01 sp007128425	76.5629	122	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	99.57	99.45	0.89	0.83	3	-
GCA_007127695.1	s__SKNL01 sp007127695	76.442	101	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	99.48	99.18	0.83	0.75	4	-
GCA_007128855.1	s__SKNL01 sp007128855	76.4407	133	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	99.27	99.27	0.81	0.81	2	-
GCA_007122185.1	s__SKNL01 sp007122185	76.3901	52	1228	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Natronogracilivirgulaceae;g__SKNL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:55,418] [INFO] GTDB search result was written to GCF_017921895.1_ASM1792189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:55,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:55,423] [INFO] DFAST_QC result json was written to GCF_017921895.1_ASM1792189v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:55,423] [INFO] DFAST_QC completed!
[2024-01-24 11:52:55,423] [INFO] Total running time: 0h1m44s