[2023-06-30 22:12:05,633] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:12:05,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:12:05,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference
[2023-06-30 22:12:08,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:12:08,190] [INFO] Task started: Prodigal
[2023-06-30 22:12:08,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg14f38381-66c3-48ba-ae5d-88b6d1ddd1b8/GCA_016708595.1_ASM1670859v1_genomic.fna.gz | prodigal -d GCA_016708595.1_ASM1670859v1_genomic.fna/cds.fna -a GCA_016708595.1_ASM1670859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:12:27,774] [INFO] Task succeeded: Prodigal
[2023-06-30 22:12:27,774] [INFO] Task started: HMMsearch
[2023-06-30 22:12:27,775] [INFO] Running command: hmmsearch --tblout GCA_016708595.1_ASM1670859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference/reference_markers.hmm GCA_016708595.1_ASM1670859v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:12:28,063] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:12:28,065] [INFO] Found 6/6 markers.
[2023-06-30 22:12:28,169] [INFO] Query marker FASTA was written to GCA_016708595.1_ASM1670859v1_genomic.fna/markers.fasta
[2023-06-30 22:12:28,170] [INFO] Task started: Blastn
[2023-06-30 22:12:28,170] [INFO] Running command: blastn -query GCA_016708595.1_ASM1670859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference/reference_markers.fasta -out GCA_016708595.1_ASM1670859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:12:28,791] [INFO] Task succeeded: Blastn
[2023-06-30 22:12:28,797] [INFO] Selected 24 target genomes.
[2023-06-30 22:12:28,798] [INFO] Target genome list was writen to GCA_016708595.1_ASM1670859v1_genomic.fna/target_genomes.txt
[2023-06-30 22:12:28,801] [INFO] Task started: fastANI
[2023-06-30 22:12:28,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg14f38381-66c3-48ba-ae5d-88b6d1ddd1b8/GCA_016708595.1_ASM1670859v1_genomic.fna.gz --refList GCA_016708595.1_ASM1670859v1_genomic.fna/target_genomes.txt --output GCA_016708595.1_ASM1670859v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:12:46,098] [INFO] Task succeeded: fastANI
[2023-06-30 22:12:46,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:12:46,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:12:46,101] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:12:46,101] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:12:46,101] [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 22:12:46,103] [INFO] DFAST Taxonomy check result was written to GCA_016708595.1_ASM1670859v1_genomic.fna/tc_result.tsv
[2023-06-30 22:12:46,104] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:12:46,104] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:12:46,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference/checkm_data
[2023-06-30 22:12:46,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:12:46,157] [INFO] Task started: CheckM
[2023-06-30 22:12:46,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708595.1_ASM1670859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708595.1_ASM1670859v1_genomic.fna/checkm_input GCA_016708595.1_ASM1670859v1_genomic.fna/checkm_result
[2023-06-30 22:13:42,820] [INFO] Task succeeded: CheckM
[2023-06-30 22:13:42,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:13:42,864] [INFO] ===== Completeness check finished =====
[2023-06-30 22:13:42,866] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:13:42,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708595.1_ASM1670859v1_genomic.fna/markers.fasta)
[2023-06-30 22:13:42,867] [INFO] Task started: Blastn
[2023-06-30 22:13:42,868] [INFO] Running command: blastn -query GCA_016708595.1_ASM1670859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68b6d40a-0bf0-417a-a56d-16fabddaa9f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708595.1_ASM1670859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:13:43,728] [INFO] Task succeeded: Blastn
[2023-06-30 22:13:43,733] [INFO] Selected 26 target genomes.
[2023-06-30 22:13:43,733] [INFO] Target genome list was writen to GCA_016708595.1_ASM1670859v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:13:43,763] [INFO] Task started: fastANI
[2023-06-30 22:13:43,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg14f38381-66c3-48ba-ae5d-88b6d1ddd1b8/GCA_016708595.1_ASM1670859v1_genomic.fna.gz --refList GCA_016708595.1_ASM1670859v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708595.1_ASM1670859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:14:01,808] [INFO] Task succeeded: fastANI
[2023-06-30 22:14:01,817] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:14:01,818] [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_016706865.1	s__UBA7236 sp002473275	98.3597	1487	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__BACL12;g__UBA7236	95.0	98.41	98.24	0.91	0.83	4	conclusive
GCA_016706255.1	s__UBA7236 sp016706255	77.7803	426	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__BACL12;g__UBA7236	95.0	98.44	98.44	0.88	0.88	2	-
GCA_016718035.1	s__UBA7236 sp016718035	77.2679	341	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__BACL12;g__UBA7236	95.0	99.00	98.46	0.95	0.93	5	-
GCA_016715425.1	s__JADKAC01 sp016715425	76.1651	121	1669	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__BACL12;g__JADKAC01	95.0	99.26	99.03	0.95	0.90	9	-
--------------------------------------------------------------------------------
[2023-06-30 22:14:01,820] [INFO] GTDB search result was written to GCA_016708595.1_ASM1670859v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:14:01,821] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:14:01,823] [INFO] DFAST_QC result json was written to GCA_016708595.1_ASM1670859v1_genomic.fna/dqc_result.json
[2023-06-30 22:14:01,824] [INFO] DFAST_QC completed!
[2023-06-30 22:14:01,824] [INFO] Total running time: 0h1m56s