[2023-06-14 01:06:54,896] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:06:54,898] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:06:54,898] [INFO] DQC Reference Directory: /var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference
[2023-06-14 01:06:56,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:06:56,117] [INFO] Task started: Prodigal
[2023-06-14 01:06:56,117] [INFO] Running command: gunzip -c /var/lib/cwl/stga9e1f53f-68f1-43c7-85e6-ae80e0c21f8e/GCA_022448955.1_ASM2244895v1_genomic.fna.gz | prodigal -d GCA_022448955.1_ASM2244895v1_genomic.fna/cds.fna -a GCA_022448955.1_ASM2244895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:19,316] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:19,317] [INFO] Task started: HMMsearch
[2023-06-14 01:07:19,317] [INFO] Running command: hmmsearch --tblout GCA_022448955.1_ASM2244895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference/reference_markers.hmm GCA_022448955.1_ASM2244895v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:19,674] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:19,676] [INFO] Found 6/6 markers.
[2023-06-14 01:07:19,739] [INFO] Query marker FASTA was written to GCA_022448955.1_ASM2244895v1_genomic.fna/markers.fasta
[2023-06-14 01:07:19,739] [INFO] Task started: Blastn
[2023-06-14 01:07:19,739] [INFO] Running command: blastn -query GCA_022448955.1_ASM2244895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference/reference_markers.fasta -out GCA_022448955.1_ASM2244895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:20,366] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:20,371] [INFO] Selected 32 target genomes.
[2023-06-14 01:07:20,371] [INFO] Target genome list was writen to GCA_022448955.1_ASM2244895v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:20,381] [INFO] Task started: fastANI
[2023-06-14 01:07:20,382] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e1f53f-68f1-43c7-85e6-ae80e0c21f8e/GCA_022448955.1_ASM2244895v1_genomic.fna.gz --refList GCA_022448955.1_ASM2244895v1_genomic.fna/target_genomes.txt --output GCA_022448955.1_ASM2244895v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:46,137] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:46,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:46,138] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:46,140] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:07:46,140] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:07:46,141] [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
--------------------------------------------------------------------------------
[2023-06-14 01:07:46,143] [INFO] DFAST Taxonomy check result was written to GCA_022448955.1_ASM2244895v1_genomic.fna/tc_result.tsv
[2023-06-14 01:07:46,144] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:46,144] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:46,144] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference/checkm_data
[2023-06-14 01:07:46,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:46,210] [INFO] Task started: CheckM
[2023-06-14 01:07:46,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448955.1_ASM2244895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448955.1_ASM2244895v1_genomic.fna/checkm_input GCA_022448955.1_ASM2244895v1_genomic.fna/checkm_result
[2023-06-14 01:08:51,742] [INFO] Task succeeded: CheckM
[2023-06-14 01:08:51,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:08:51,767] [INFO] ===== Completeness check finished =====
[2023-06-14 01:08:51,768] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:08:51,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448955.1_ASM2244895v1_genomic.fna/markers.fasta)
[2023-06-14 01:08:51,768] [INFO] Task started: Blastn
[2023-06-14 01:08:51,769] [INFO] Running command: blastn -query GCA_022448955.1_ASM2244895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge832da19-e55d-4300-a168-1c3883fd914f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448955.1_ASM2244895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:08:52,504] [INFO] Task succeeded: Blastn
[2023-06-14 01:08:52,510] [INFO] Selected 35 target genomes.
[2023-06-14 01:08:52,510] [INFO] Target genome list was writen to GCA_022448955.1_ASM2244895v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:08:52,559] [INFO] Task started: fastANI
[2023-06-14 01:08:52,559] [INFO] Running command: fastANI --query /var/lib/cwl/stga9e1f53f-68f1-43c7-85e6-ae80e0c21f8e/GCA_022448955.1_ASM2244895v1_genomic.fna.gz --refList GCA_022448955.1_ASM2244895v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448955.1_ASM2244895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:09:16,183] [INFO] Task succeeded: fastANI
[2023-06-14 01:09:16,189] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:09:16,189] [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_013214355.1	s__DT-111 sp013214355	75.5192	61	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__DT-111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857395.1	s__JAFMDF01 sp017857395	75.1826	65	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__JAFMDF01	95.0	99.01	98.09	0.88	0.83	3	-
GCA_905480595.1	s__CAJQQY01 sp905480595	75.0051	66	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__CAJQQY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:09:16,191] [INFO] GTDB search result was written to GCA_022448955.1_ASM2244895v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:09:16,191] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:09:16,194] [INFO] DFAST_QC result json was written to GCA_022448955.1_ASM2244895v1_genomic.fna/dqc_result.json
[2023-06-14 01:09:16,194] [INFO] DFAST_QC completed!
[2023-06-14 01:09:16,194] [INFO] Total running time: 0h2m21s