[2023-06-30 13:06:03,401] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:06:03,405] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:06:03,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference
[2023-06-30 13:06:05,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:06:05,748] [INFO] Task started: Prodigal
[2023-06-30 13:06:05,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d80e5f5-196b-4e83-a1ec-403b34794e7d/GCA_016779005.1_ASM1677900v1_genomic.fna.gz | prodigal -d GCA_016779005.1_ASM1677900v1_genomic.fna/cds.fna -a GCA_016779005.1_ASM1677900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:06:09,984] [INFO] Task succeeded: Prodigal
[2023-06-30 13:06:09,984] [INFO] Task started: HMMsearch
[2023-06-30 13:06:09,984] [INFO] Running command: hmmsearch --tblout GCA_016779005.1_ASM1677900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference/reference_markers.hmm GCA_016779005.1_ASM1677900v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:06:10,226] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:06:10,228] [INFO] Found 6/6 markers.
[2023-06-30 13:06:10,251] [INFO] Query marker FASTA was written to GCA_016779005.1_ASM1677900v1_genomic.fna/markers.fasta
[2023-06-30 13:06:10,252] [INFO] Task started: Blastn
[2023-06-30 13:06:10,252] [INFO] Running command: blastn -query GCA_016779005.1_ASM1677900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference/reference_markers.fasta -out GCA_016779005.1_ASM1677900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:06:11,283] [INFO] Task succeeded: Blastn
[2023-06-30 13:06:11,287] [INFO] Selected 20 target genomes.
[2023-06-30 13:06:11,287] [INFO] Target genome list was writen to GCA_016779005.1_ASM1677900v1_genomic.fna/target_genomes.txt
[2023-06-30 13:06:11,294] [INFO] Task started: fastANI
[2023-06-30 13:06:11,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d80e5f5-196b-4e83-a1ec-403b34794e7d/GCA_016779005.1_ASM1677900v1_genomic.fna.gz --refList GCA_016779005.1_ASM1677900v1_genomic.fna/target_genomes.txt --output GCA_016779005.1_ASM1677900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:06:21,804] [INFO] Task succeeded: fastANI
[2023-06-30 13:06:21,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:06:21,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:06:21,808] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:06:21,808] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 13:06:21,808] [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 13:06:21,810] [INFO] DFAST Taxonomy check result was written to GCA_016779005.1_ASM1677900v1_genomic.fna/tc_result.tsv
[2023-06-30 13:06:21,811] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:06:21,812] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:06:21,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference/checkm_data
[2023-06-30 13:06:21,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:06:21,842] [INFO] Task started: CheckM
[2023-06-30 13:06:21,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016779005.1_ASM1677900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016779005.1_ASM1677900v1_genomic.fna/checkm_input GCA_016779005.1_ASM1677900v1_genomic.fna/checkm_result
[2023-06-30 13:06:41,549] [INFO] Task succeeded: CheckM
[2023-06-30 13:06:41,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:06:41,575] [INFO] ===== Completeness check finished =====
[2023-06-30 13:06:41,575] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:06:41,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016779005.1_ASM1677900v1_genomic.fna/markers.fasta)
[2023-06-30 13:06:41,576] [INFO] Task started: Blastn
[2023-06-30 13:06:41,576] [INFO] Running command: blastn -query GCA_016779005.1_ASM1677900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a27d244-4426-496c-8fd2-4c1f95964022/dqc_reference/reference_markers_gtdb.fasta -out GCA_016779005.1_ASM1677900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:06:42,574] [INFO] Task succeeded: Blastn
[2023-06-30 13:06:42,579] [INFO] Selected 19 target genomes.
[2023-06-30 13:06:42,580] [INFO] Target genome list was writen to GCA_016779005.1_ASM1677900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:06:42,594] [INFO] Task started: fastANI
[2023-06-30 13:06:42,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d80e5f5-196b-4e83-a1ec-403b34794e7d/GCA_016779005.1_ASM1677900v1_genomic.fna.gz --refList GCA_016779005.1_ASM1677900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016779005.1_ASM1677900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:06:49,245] [INFO] Task succeeded: fastANI
[2023-06-30 13:06:49,251] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:06:49,251] [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_016779005.1	s__UBA5951 sp016779005	100.0	629	631	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	96.62	95.51	0.89	0.87	4	conclusive
GCA_009936885.1	s__UBA5951 sp009936885	94.4553	362	631	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902516825.1	s__UBA5951 sp902516825	86.2229	318	631	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666135.1	s__UBA5951 sp018666135	77.9333	216	631	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	99.32	99.32	0.87	0.87	2	-
GCA_012269555.1	s__UBA5951 sp012269555	77.2131	156	631	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA5951	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:06:49,253] [INFO] GTDB search result was written to GCA_016779005.1_ASM1677900v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:06:49,254] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:06:49,256] [INFO] DFAST_QC result json was written to GCA_016779005.1_ASM1677900v1_genomic.fna/dqc_result.json
[2023-06-30 13:06:49,256] [INFO] DFAST_QC completed!
[2023-06-30 13:06:49,257] [INFO] Total running time: 0h0m46s