[2023-06-16 19:17:28,870] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:17:28,880] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:17:28,880] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference
[2023-06-16 19:17:30,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:17:30,085] [INFO] Task started: Prodigal
[2023-06-16 19:17:30,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg9613d38d-0226-4935-ad23-a0081fe5763b/GCA_009992855.1_ASM999285v1_genomic.fna.gz | prodigal -d GCA_009992855.1_ASM999285v1_genomic.fna/cds.fna -a GCA_009992855.1_ASM999285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:17:43,900] [INFO] Task succeeded: Prodigal
[2023-06-16 19:17:43,900] [INFO] Task started: HMMsearch
[2023-06-16 19:17:43,900] [INFO] Running command: hmmsearch --tblout GCA_009992855.1_ASM999285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference/reference_markers.hmm GCA_009992855.1_ASM999285v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:17:44,240] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:17:44,241] [INFO] Found 6/6 markers.
[2023-06-16 19:17:44,290] [INFO] Query marker FASTA was written to GCA_009992855.1_ASM999285v1_genomic.fna/markers.fasta
[2023-06-16 19:17:44,290] [INFO] Task started: Blastn
[2023-06-16 19:17:44,291] [INFO] Running command: blastn -query GCA_009992855.1_ASM999285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference/reference_markers.fasta -out GCA_009992855.1_ASM999285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:17:44,832] [INFO] Task succeeded: Blastn
[2023-06-16 19:17:44,836] [INFO] Selected 16 target genomes.
[2023-06-16 19:17:44,836] [INFO] Target genome list was writen to GCA_009992855.1_ASM999285v1_genomic.fna/target_genomes.txt
[2023-06-16 19:17:44,838] [INFO] Task started: fastANI
[2023-06-16 19:17:44,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg9613d38d-0226-4935-ad23-a0081fe5763b/GCA_009992855.1_ASM999285v1_genomic.fna.gz --refList GCA_009992855.1_ASM999285v1_genomic.fna/target_genomes.txt --output GCA_009992855.1_ASM999285v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:17:56,817] [INFO] Task succeeded: fastANI
[2023-06-16 19:17:56,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:17:56,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:17:56,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:17:56,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:17:56,819] [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
--------------------------------------------------------------------------------
[2023-06-16 19:17:56,820] [INFO] DFAST Taxonomy check result was written to GCA_009992855.1_ASM999285v1_genomic.fna/tc_result.tsv
[2023-06-16 19:17:56,821] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:17:56,821] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:17:56,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference/checkm_data
[2023-06-16 19:17:56,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:17:56,897] [INFO] Task started: CheckM
[2023-06-16 19:17:56,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009992855.1_ASM999285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009992855.1_ASM999285v1_genomic.fna/checkm_input GCA_009992855.1_ASM999285v1_genomic.fna/checkm_result
[2023-06-16 19:18:38,453] [INFO] Task succeeded: CheckM
[2023-06-16 19:18:38,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:18:38,473] [INFO] ===== Completeness check finished =====
[2023-06-16 19:18:38,473] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:18:38,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009992855.1_ASM999285v1_genomic.fna/markers.fasta)
[2023-06-16 19:18:38,474] [INFO] Task started: Blastn
[2023-06-16 19:18:38,474] [INFO] Running command: blastn -query GCA_009992855.1_ASM999285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3f30b4e-c2b3-4b8e-b436-bdaf0776d534/dqc_reference/reference_markers_gtdb.fasta -out GCA_009992855.1_ASM999285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:18:39,229] [INFO] Task succeeded: Blastn
[2023-06-16 19:18:39,232] [INFO] Selected 18 target genomes.
[2023-06-16 19:18:39,232] [INFO] Target genome list was writen to GCA_009992855.1_ASM999285v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:18:39,245] [INFO] Task started: fastANI
[2023-06-16 19:18:39,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg9613d38d-0226-4935-ad23-a0081fe5763b/GCA_009992855.1_ASM999285v1_genomic.fna.gz --refList GCA_009992855.1_ASM999285v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009992855.1_ASM999285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:18:53,367] [INFO] Task succeeded: fastANI
[2023-06-16 19:18:53,370] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:18:53,371] [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_001872605.1	s__CG2-30-59-28 sp001872605	99.7976	1451	1567	d__Bacteria;p__Armatimonadota;c__Abditibacteria;o__CG2-30-59-28;f__CG2-30-59-28;g__CG2-30-59-28	95.0	99.82	99.73	0.89	0.86	5	conclusive
GCA_016199605.1	s__JACQGJ01 sp016199605	77.3273	79	1567	d__Bacteria;p__Armatimonadota;c__Abditibacteria;o__CG2-30-59-28;f__CG2-30-59-28;g__JACQGJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:18:53,373] [INFO] GTDB search result was written to GCA_009992855.1_ASM999285v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:18:53,373] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:18:53,375] [INFO] DFAST_QC result json was written to GCA_009992855.1_ASM999285v1_genomic.fna/dqc_result.json
[2023-06-16 19:18:53,375] [INFO] DFAST_QC completed!
[2023-06-16 19:18:53,375] [INFO] Total running time: 0h1m25s