[2023-06-29 12:50:34,281] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:50:34,283] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:50:34,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference
[2023-06-29 12:50:35,454] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:50:35,454] [INFO] Task started: Prodigal
[2023-06-29 12:50:35,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg454d465d-ae38-4401-92c1-696d9ea15553/GCA_011043455.1_ASM1104345v1_genomic.fna.gz | prodigal -d GCA_011043455.1_ASM1104345v1_genomic.fna/cds.fna -a GCA_011043455.1_ASM1104345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:50:41,548] [INFO] Task succeeded: Prodigal
[2023-06-29 12:50:41,548] [INFO] Task started: HMMsearch
[2023-06-29 12:50:41,549] [INFO] Running command: hmmsearch --tblout GCA_011043455.1_ASM1104345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference/reference_markers.hmm GCA_011043455.1_ASM1104345v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:50:41,782] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:50:41,783] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg454d465d-ae38-4401-92c1-696d9ea15553/GCA_011043455.1_ASM1104345v1_genomic.fna.gz]
[2023-06-29 12:50:41,810] [INFO] Query marker FASTA was written to GCA_011043455.1_ASM1104345v1_genomic.fna/markers.fasta
[2023-06-29 12:50:41,811] [INFO] Task started: Blastn
[2023-06-29 12:50:41,811] [INFO] Running command: blastn -query GCA_011043455.1_ASM1104345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference/reference_markers.fasta -out GCA_011043455.1_ASM1104345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:50:42,359] [INFO] Task succeeded: Blastn
[2023-06-29 12:50:42,364] [INFO] Selected 15 target genomes.
[2023-06-29 12:50:42,364] [INFO] Target genome list was writen to GCA_011043455.1_ASM1104345v1_genomic.fna/target_genomes.txt
[2023-06-29 12:50:42,368] [INFO] Task started: fastANI
[2023-06-29 12:50:42,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg454d465d-ae38-4401-92c1-696d9ea15553/GCA_011043455.1_ASM1104345v1_genomic.fna.gz --refList GCA_011043455.1_ASM1104345v1_genomic.fna/target_genomes.txt --output GCA_011043455.1_ASM1104345v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:50:49,852] [INFO] Task succeeded: fastANI
[2023-06-29 12:50:49,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:50:49,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:50:49,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:50:49,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:50:49,856] [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
--------------------------------------------------------------------------------
[2023-06-29 12:50:49,859] [INFO] DFAST Taxonomy check result was written to GCA_011043455.1_ASM1104345v1_genomic.fna/tc_result.tsv
[2023-06-29 12:50:49,859] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:50:49,859] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:50:49,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference/checkm_data
[2023-06-29 12:50:49,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:50:49,897] [INFO] Task started: CheckM
[2023-06-29 12:50:49,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011043455.1_ASM1104345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011043455.1_ASM1104345v1_genomic.fna/checkm_input GCA_011043455.1_ASM1104345v1_genomic.fna/checkm_result
[2023-06-29 12:51:14,927] [INFO] Task succeeded: CheckM
[2023-06-29 12:51:14,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:51:14,951] [INFO] ===== Completeness check finished =====
[2023-06-29 12:51:14,951] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:51:14,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011043455.1_ASM1104345v1_genomic.fna/markers.fasta)
[2023-06-29 12:51:14,952] [INFO] Task started: Blastn
[2023-06-29 12:51:14,952] [INFO] Running command: blastn -query GCA_011043455.1_ASM1104345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9913cd20-7023-416e-9d37-21718ba971bc/dqc_reference/reference_markers_gtdb.fasta -out GCA_011043455.1_ASM1104345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:51:15,638] [INFO] Task succeeded: Blastn
[2023-06-29 12:51:15,643] [INFO] Selected 11 target genomes.
[2023-06-29 12:51:15,643] [INFO] Target genome list was writen to GCA_011043455.1_ASM1104345v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:51:15,656] [INFO] Task started: fastANI
[2023-06-29 12:51:15,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg454d465d-ae38-4401-92c1-696d9ea15553/GCA_011043455.1_ASM1104345v1_genomic.fna.gz --refList GCA_011043455.1_ASM1104345v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011043455.1_ASM1104345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:51:31,765] [INFO] Task succeeded: fastANI
[2023-06-29 12:51:31,775] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:51:31,776] [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_003645185.1	s__UBA10656 sp003645185	99.0039	750	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__UBA10656	95.0	99.64	99.64	0.90	0.90	2	conclusive
GCA_002085445.1	s__UBA10656 sp002085445	80.715	293	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__UBA10656	95.0	99.66	99.66	0.86	0.86	2	-
GCA_000785145.2	s__Thiomargarita nelsonii_B	77.2099	157	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__Thiomargarita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003645255.1	s__QNES01 sp003645255	77.0104	139	841	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Beggiatoales;f__Beggiatoaceae;g__QNES01	95.0	99.58	99.49	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 12:51:31,778] [INFO] GTDB search result was written to GCA_011043455.1_ASM1104345v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:51:31,779] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:51:31,782] [INFO] DFAST_QC result json was written to GCA_011043455.1_ASM1104345v1_genomic.fna/dqc_result.json
[2023-06-29 12:51:31,783] [INFO] DFAST_QC completed!
[2023-06-29 12:51:31,783] [INFO] Total running time: 0h0m58s