[2023-06-30 08:13:26,801] [INFO] DFAST_QC pipeline started.
[2023-06-30 08:13:26,803] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 08:13:26,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference
[2023-06-30 08:13:29,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 08:13:29,112] [INFO] Task started: Prodigal
[2023-06-30 08:13:29,112] [INFO] Running command: gunzip -c /var/lib/cwl/stga1100025-d483-4796-90d6-64050ff4e852/GCA_016930635.1_ASM1693063v1_genomic.fna.gz | prodigal -d GCA_016930635.1_ASM1693063v1_genomic.fna/cds.fna -a GCA_016930635.1_ASM1693063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 08:13:34,263] [INFO] Task succeeded: Prodigal
[2023-06-30 08:13:34,263] [INFO] Task started: HMMsearch
[2023-06-30 08:13:34,264] [INFO] Running command: hmmsearch --tblout GCA_016930635.1_ASM1693063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference/reference_markers.hmm GCA_016930635.1_ASM1693063v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 08:13:34,507] [INFO] Task succeeded: HMMsearch
[2023-06-30 08:13:34,508] [INFO] Found 6/6 markers.
[2023-06-30 08:13:34,534] [INFO] Query marker FASTA was written to GCA_016930635.1_ASM1693063v1_genomic.fna/markers.fasta
[2023-06-30 08:13:34,534] [INFO] Task started: Blastn
[2023-06-30 08:13:34,535] [INFO] Running command: blastn -query GCA_016930635.1_ASM1693063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference/reference_markers.fasta -out GCA_016930635.1_ASM1693063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:13:35,107] [INFO] Task succeeded: Blastn
[2023-06-30 08:13:35,111] [INFO] Selected 12 target genomes.
[2023-06-30 08:13:35,112] [INFO] Target genome list was writen to GCA_016930635.1_ASM1693063v1_genomic.fna/target_genomes.txt
[2023-06-30 08:13:35,118] [INFO] Task started: fastANI
[2023-06-30 08:13:35,118] [INFO] Running command: fastANI --query /var/lib/cwl/stga1100025-d483-4796-90d6-64050ff4e852/GCA_016930635.1_ASM1693063v1_genomic.fna.gz --refList GCA_016930635.1_ASM1693063v1_genomic.fna/target_genomes.txt --output GCA_016930635.1_ASM1693063v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 08:13:41,388] [INFO] Task succeeded: fastANI
[2023-06-30 08:13:41,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 08:13:41,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 08:13:41,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 08:13:41,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 08:13:41,393] [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 08:13:41,395] [INFO] DFAST Taxonomy check result was written to GCA_016930635.1_ASM1693063v1_genomic.fna/tc_result.tsv
[2023-06-30 08:13:41,396] [INFO] ===== Taxonomy check completed =====
[2023-06-30 08:13:41,396] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 08:13:41,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference/checkm_data
[2023-06-30 08:13:41,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 08:13:41,431] [INFO] Task started: CheckM
[2023-06-30 08:13:41,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016930635.1_ASM1693063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016930635.1_ASM1693063v1_genomic.fna/checkm_input GCA_016930635.1_ASM1693063v1_genomic.fna/checkm_result
[2023-06-30 08:14:04,151] [INFO] Task succeeded: CheckM
[2023-06-30 08:14:04,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 08:14:04,176] [INFO] ===== Completeness check finished =====
[2023-06-30 08:14:04,176] [INFO] ===== Start GTDB Search =====
[2023-06-30 08:14:04,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016930635.1_ASM1693063v1_genomic.fna/markers.fasta)
[2023-06-30 08:14:04,177] [INFO] Task started: Blastn
[2023-06-30 08:14:04,177] [INFO] Running command: blastn -query GCA_016930635.1_ASM1693063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25085c4f-de1e-4896-9895-6704c6955ecd/dqc_reference/reference_markers_gtdb.fasta -out GCA_016930635.1_ASM1693063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:14:04,964] [INFO] Task succeeded: Blastn
[2023-06-30 08:14:04,969] [INFO] Selected 16 target genomes.
[2023-06-30 08:14:04,969] [INFO] Target genome list was writen to GCA_016930635.1_ASM1693063v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 08:14:04,985] [INFO] Task started: fastANI
[2023-06-30 08:14:04,985] [INFO] Running command: fastANI --query /var/lib/cwl/stga1100025-d483-4796-90d6-64050ff4e852/GCA_016930635.1_ASM1693063v1_genomic.fna.gz --refList GCA_016930635.1_ASM1693063v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016930635.1_ASM1693063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:14:13,895] [INFO] Task succeeded: fastANI
[2023-06-30 08:14:13,906] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:14:13,906] [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_016930635.1	s__JAFGGI01 sp016930635	100.0	785	790	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__UBA12454;g__JAFGGI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018828825.1	s__UBA12454 sp018828825	76.9017	137	790	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__UBA12454;g__UBA12454	95.0	99.85	99.71	0.95	0.90	4	-
GCA_903847315.1	s__UBA12454 sp903847315	76.4244	105	790	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__UBA12454;g__UBA12454	95.0	99.97	99.96	0.97	0.97	3	-
GCA_002839495.1	s__UBA12454 sp002839495	76.4131	106	790	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__UBA12454;g__UBA12454	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142595.1	s__UBA12454 sp003142595	76.1762	86	790	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__UBA12454;g__UBA12454	95.0	99.83	99.72	0.98	0.98	3	-
GCA_001825665.1	s__UBA12454 sp001825665	75.7055	62	790	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Sedimentisphaerales;f__UBA12454;g__UBA12454	95.0	99.94	99.94	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-30 08:14:13,909] [INFO] GTDB search result was written to GCA_016930635.1_ASM1693063v1_genomic.fna/result_gtdb.tsv
[2023-06-30 08:14:13,909] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:14:13,912] [INFO] DFAST_QC result json was written to GCA_016930635.1_ASM1693063v1_genomic.fna/dqc_result.json
[2023-06-30 08:14:13,912] [INFO] DFAST_QC completed!
[2023-06-30 08:14:13,912] [INFO] Total running time: 0h0m47s