[2023-06-17 01:29:04,778] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:29:04,780] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:29:04,780] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference
[2023-06-17 01:29:06,025] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:29:06,026] [INFO] Task started: Prodigal
[2023-06-17 01:29:06,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg05ad0c76-d969-4061-a268-b894d52658f3/GCA_028277345.1_ASM2827734v1_genomic.fna.gz | prodigal -d GCA_028277345.1_ASM2827734v1_genomic.fna/cds.fna -a GCA_028277345.1_ASM2827734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:29:14,540] [INFO] Task succeeded: Prodigal
[2023-06-17 01:29:14,541] [INFO] Task started: HMMsearch
[2023-06-17 01:29:14,541] [INFO] Running command: hmmsearch --tblout GCA_028277345.1_ASM2827734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference/reference_markers.hmm GCA_028277345.1_ASM2827734v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:29:14,801] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:29:14,803] [INFO] Found 6/6 markers.
[2023-06-17 01:29:14,830] [INFO] Query marker FASTA was written to GCA_028277345.1_ASM2827734v1_genomic.fna/markers.fasta
[2023-06-17 01:29:14,830] [INFO] Task started: Blastn
[2023-06-17 01:29:14,830] [INFO] Running command: blastn -query GCA_028277345.1_ASM2827734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference/reference_markers.fasta -out GCA_028277345.1_ASM2827734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:15,443] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:15,447] [INFO] Selected 14 target genomes.
[2023-06-17 01:29:15,447] [INFO] Target genome list was writen to GCA_028277345.1_ASM2827734v1_genomic.fna/target_genomes.txt
[2023-06-17 01:29:15,451] [INFO] Task started: fastANI
[2023-06-17 01:29:15,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg05ad0c76-d969-4061-a268-b894d52658f3/GCA_028277345.1_ASM2827734v1_genomic.fna.gz --refList GCA_028277345.1_ASM2827734v1_genomic.fna/target_genomes.txt --output GCA_028277345.1_ASM2827734v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:29:24,564] [INFO] Task succeeded: fastANI
[2023-06-17 01:29:24,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:29:24,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:29:24,568] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:29:24,568] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:29:24,568] [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
--------------------------------------------------------------------------------
[2023-06-17 01:29:24,570] [INFO] DFAST Taxonomy check result was written to GCA_028277345.1_ASM2827734v1_genomic.fna/tc_result.tsv
[2023-06-17 01:29:24,571] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:29:24,571] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:29:24,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference/checkm_data
[2023-06-17 01:29:24,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:29:24,617] [INFO] Task started: CheckM
[2023-06-17 01:29:24,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028277345.1_ASM2827734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028277345.1_ASM2827734v1_genomic.fna/checkm_input GCA_028277345.1_ASM2827734v1_genomic.fna/checkm_result
[2023-06-17 01:29:55,829] [INFO] Task succeeded: CheckM
[2023-06-17 01:29:55,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:29:55,855] [INFO] ===== Completeness check finished =====
[2023-06-17 01:29:55,856] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:29:55,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028277345.1_ASM2827734v1_genomic.fna/markers.fasta)
[2023-06-17 01:29:55,856] [INFO] Task started: Blastn
[2023-06-17 01:29:55,857] [INFO] Running command: blastn -query GCA_028277345.1_ASM2827734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c05f33a-970b-48b6-ac58-914f0bfa551a/dqc_reference/reference_markers_gtdb.fasta -out GCA_028277345.1_ASM2827734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:56,677] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:56,682] [INFO] Selected 20 target genomes.
[2023-06-17 01:29:56,683] [INFO] Target genome list was writen to GCA_028277345.1_ASM2827734v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:29:56,696] [INFO] Task started: fastANI
[2023-06-17 01:29:56,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg05ad0c76-d969-4061-a268-b894d52658f3/GCA_028277345.1_ASM2827734v1_genomic.fna.gz --refList GCA_028277345.1_ASM2827734v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028277345.1_ASM2827734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:30:05,242] [INFO] Task succeeded: fastANI
[2023-06-17 01:30:05,248] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 01:30:05,249] [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_018817505.1	s__SPBW01 sp018817505	77.8954	92	905	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__UBA7950;f__UBA9294;g__SPBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004525685.1	s__SPBW01 sp004525685	77.6682	107	905	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__UBA7950;f__UBA9294;g__SPBW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:30:05,251] [INFO] GTDB search result was written to GCA_028277345.1_ASM2827734v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:30:05,252] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:30:05,254] [INFO] DFAST_QC result json was written to GCA_028277345.1_ASM2827734v1_genomic.fna/dqc_result.json
[2023-06-17 01:30:05,254] [INFO] DFAST_QC completed!
[2023-06-17 01:30:05,254] [INFO] Total running time: 0h1m0s