[2023-06-13 02:32:33,174] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:33,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:33,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference
[2023-06-13 02:32:34,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:34,405] [INFO] Task started: Prodigal
[2023-06-13 02:32:34,405] [INFO] Running command: gunzip -c /var/lib/cwl/stg27c22b4a-9377-428e-bd10-fb9285e63512/GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna.gz | prodigal -d GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/cds.fna -a GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:36,263] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:36,263] [INFO] Task started: HMMsearch
[2023-06-13 02:32:36,263] [INFO] Running command: hmmsearch --tblout GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference/reference_markers.hmm GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:36,448] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:36,450] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27c22b4a-9377-428e-bd10-fb9285e63512/GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna.gz]
[2023-06-13 02:32:36,468] [INFO] Query marker FASTA was written to GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/markers.fasta
[2023-06-13 02:32:36,469] [INFO] Task started: Blastn
[2023-06-13 02:32:36,469] [INFO] Running command: blastn -query GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference/reference_markers.fasta -out GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:39,167] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:39,173] [INFO] Selected 10 target genomes.
[2023-06-13 02:32:39,173] [INFO] Target genome list was writen to GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/target_genomes.txt
[2023-06-13 02:32:39,192] [INFO] Task started: fastANI
[2023-06-13 02:32:39,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c22b4a-9377-428e-bd10-fb9285e63512/GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna.gz --refList GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/target_genomes.txt --output GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:32:44,385] [INFO] Task succeeded: fastANI
[2023-06-13 02:32:44,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:32:44,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:32:44,387] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:32:44,387] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 02:32:44,388] [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 02:32:44,389] [INFO] DFAST Taxonomy check result was written to GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/tc_result.tsv
[2023-06-13 02:32:44,390] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:32:44,390] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:32:44,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference/checkm_data
[2023-06-13 02:32:44,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:32:44,404] [INFO] Task started: CheckM
[2023-06-13 02:32:44,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/checkm_input GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/checkm_result
[2023-06-13 02:32:58,895] [INFO] Task succeeded: CheckM
[2023-06-13 02:32:58,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:32:58,919] [INFO] ===== Completeness check finished =====
[2023-06-13 02:32:58,919] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:32:58,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/markers.fasta)
[2023-06-13 02:32:58,920] [INFO] Task started: Blastn
[2023-06-13 02:32:58,920] [INFO] Running command: blastn -query GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0b1189e-2972-48a3-9174-1d61d8675336/dqc_reference/reference_markers_gtdb.fasta -out GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:59,933] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:59,937] [INFO] Selected 14 target genomes.
[2023-06-13 02:32:59,938] [INFO] Target genome list was writen to GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:32:59,949] [INFO] Task started: fastANI
[2023-06-13 02:32:59,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c22b4a-9377-428e-bd10-fb9285e63512/GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna.gz --refList GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:05,946] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:05,950] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 02:33:05,950] [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_003503995.1	s__UBA9215 sp003503995	82.8506	137	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caedimonadales;f__UBA9215;g__UBA9215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993885.1	s__UBA9215 sp009993885	80.5836	119	197	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caedimonadales;f__UBA9215;g__UBA9215	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:05,952] [INFO] GTDB search result was written to GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:05,953] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:05,955] [INFO] DFAST_QC result json was written to GCA_938082405.1_S4_Bin_Bin_119_1_genomic.fna/dqc_result.json
[2023-06-13 02:33:05,956] [INFO] DFAST_QC completed!
[2023-06-13 02:33:05,956] [INFO] Total running time: 0h0m33s