[2023-06-08 02:20:11,184] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:11,187] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:11,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference
[2023-06-08 02:20:12,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:12,451] [INFO] Task started: Prodigal
[2023-06-08 02:20:12,451] [INFO] Running command: gunzip -c /var/lib/cwl/stga84692ae-a641-4986-9657-9027c383887d/GCA_902614175.1_AG-891-J18_genomic.fna.gz | prodigal -d GCA_902614175.1_AG-891-J18_genomic.fna/cds.fna -a GCA_902614175.1_AG-891-J18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:16,208] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:16,208] [INFO] Task started: HMMsearch
[2023-06-08 02:20:16,208] [INFO] Running command: hmmsearch --tblout GCA_902614175.1_AG-891-J18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference/reference_markers.hmm GCA_902614175.1_AG-891-J18_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:16,456] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:16,458] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga84692ae-a641-4986-9657-9027c383887d/GCA_902614175.1_AG-891-J18_genomic.fna.gz]
[2023-06-08 02:20:16,477] [INFO] Query marker FASTA was written to GCA_902614175.1_AG-891-J18_genomic.fna/markers.fasta
[2023-06-08 02:20:16,477] [INFO] Task started: Blastn
[2023-06-08 02:20:16,478] [INFO] Running command: blastn -query GCA_902614175.1_AG-891-J18_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference/reference_markers.fasta -out GCA_902614175.1_AG-891-J18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:17,078] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:17,082] [INFO] Selected 15 target genomes.
[2023-06-08 02:20:17,082] [INFO] Target genome list was writen to GCA_902614175.1_AG-891-J18_genomic.fna/target_genomes.txt
[2023-06-08 02:20:17,085] [INFO] Task started: fastANI
[2023-06-08 02:20:17,085] [INFO] Running command: fastANI --query /var/lib/cwl/stga84692ae-a641-4986-9657-9027c383887d/GCA_902614175.1_AG-891-J18_genomic.fna.gz --refList GCA_902614175.1_AG-891-J18_genomic.fna/target_genomes.txt --output GCA_902614175.1_AG-891-J18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:22,774] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:22,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:22,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:22,777] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:22,777] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 02:20:22,777] [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
--------------------------------------------------------------------------------
[2023-06-08 02:20:22,780] [INFO] DFAST Taxonomy check result was written to GCA_902614175.1_AG-891-J18_genomic.fna/tc_result.tsv
[2023-06-08 02:20:22,780] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:22,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:22,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference/checkm_data
[2023-06-08 02:20:22,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:22,801] [INFO] Task started: CheckM
[2023-06-08 02:20:22,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614175.1_AG-891-J18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614175.1_AG-891-J18_genomic.fna/checkm_input GCA_902614175.1_AG-891-J18_genomic.fna/checkm_result
[2023-06-08 02:20:41,433] [INFO] Task succeeded: CheckM
[2023-06-08 02:20:41,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:20:41,463] [INFO] ===== Completeness check finished =====
[2023-06-08 02:20:41,463] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:20:41,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614175.1_AG-891-J18_genomic.fna/markers.fasta)
[2023-06-08 02:20:41,464] [INFO] Task started: Blastn
[2023-06-08 02:20:41,464] [INFO] Running command: blastn -query GCA_902614175.1_AG-891-J18_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e5cdfa8-67b2-4884-97ec-581820d454e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614175.1_AG-891-J18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:42,218] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:42,224] [INFO] Selected 19 target genomes.
[2023-06-08 02:20:42,224] [INFO] Target genome list was writen to GCA_902614175.1_AG-891-J18_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:20:42,231] [INFO] Task started: fastANI
[2023-06-08 02:20:42,231] [INFO] Running command: fastANI --query /var/lib/cwl/stga84692ae-a641-4986-9657-9027c383887d/GCA_902614175.1_AG-891-J18_genomic.fna.gz --refList GCA_902614175.1_AG-891-J18_genomic.fna/target_genomes_gtdb.txt --output GCA_902614175.1_AG-891-J18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:20:46,737] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:46,755] [INFO] Found 16 fastANI hits (4 hits with ANI > circumscription radius)
[2023-06-08 02:20:46,755] [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_902546975.1	s__HIMB59 sp902546975	95.8231	332	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.15	95.57	0.84	0.81	5	inconclusive
GCA_902524245.1	s__HIMB59 sp902524245	95.4794	359	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.23	0.87	0.86	3	inconclusive
GCA_902538085.1	s__HIMB59 sp902538085	95.3366	316	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.32	95.03	0.79	0.77	3	inconclusive
GCA_902613845.1	s__HIMB59 sp902613845	95.067	341	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.34	95.19	0.82	0.79	7	inconclusive
GCA_902574995.1	s__HIMB59 sp902574995	94.7094	315	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003281065.1	s__HIMB59 sp003281065	94.4891	201	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902518505.1	s__HIMB59 sp902518505	94.4283	300	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.57	95.11	0.80	0.80	4	-
GCA_902613185.1	s__HIMB59 sp902613185	94.3607	333	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.61	99.58	0.93	0.92	5	-
GCA_902521485.1	s__HIMB59 sp902521485	94.0594	305	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	98.22	98.22	0.76	0.76	2	-
GCA_902530745.1	s__HIMB59 sp902530745	94.0542	320	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.01	95.70	0.83	0.77	8	-
GCA_902521465.1	s__HIMB59 sp902521465	94.0437	338	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.86	99.86	0.95	0.95	2	-
GCA_902621205.1	s__HIMB59 sp902621205	93.9679	321	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.28	98.69	0.88	0.86	4	-
GCA_902591315.1	s__HIMB59 sp902591315	93.716	242	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.30	0.78	0.78	2	-
GCA_902543855.1	s__HIMB59 sp902543855	93.2393	170	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.86	99.86	0.80	0.80	2	-
GCA_902601865.1	s__HIMB59 sp902601865	83.1895	272	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299115.1	s__HIMB59 sp000299115	78.4409	169	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:20:46,758] [INFO] GTDB search result was written to GCA_902614175.1_AG-891-J18_genomic.fna/result_gtdb.tsv
[2023-06-08 02:20:46,759] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:20:46,764] [INFO] DFAST_QC result json was written to GCA_902614175.1_AG-891-J18_genomic.fna/dqc_result.json
[2023-06-08 02:20:46,764] [INFO] DFAST_QC completed!
[2023-06-08 02:20:46,764] [INFO] Total running time: 0h0m36s