[2023-06-28 18:41:23,402] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:41:23,405] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:41:23,406] [INFO] DQC Reference Directory: /var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference
[2023-06-28 18:41:24,799] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:41:24,800] [INFO] Task started: Prodigal
[2023-06-28 18:41:24,800] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8bc4b97-54b3-4f6a-a079-231721c2a40a/GCA_017559615.1_ASM1755961v1_genomic.fna.gz | prodigal -d GCA_017559615.1_ASM1755961v1_genomic.fna/cds.fna -a GCA_017559615.1_ASM1755961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:41:34,733] [INFO] Task succeeded: Prodigal
[2023-06-28 18:41:34,733] [INFO] Task started: HMMsearch
[2023-06-28 18:41:34,734] [INFO] Running command: hmmsearch --tblout GCA_017559615.1_ASM1755961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference/reference_markers.hmm GCA_017559615.1_ASM1755961v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:41:34,972] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:41:34,974] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc8bc4b97-54b3-4f6a-a079-231721c2a40a/GCA_017559615.1_ASM1755961v1_genomic.fna.gz]
[2023-06-28 18:41:34,997] [INFO] Query marker FASTA was written to GCA_017559615.1_ASM1755961v1_genomic.fna/markers.fasta
[2023-06-28 18:41:34,997] [INFO] Task started: Blastn
[2023-06-28 18:41:34,998] [INFO] Running command: blastn -query GCA_017559615.1_ASM1755961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference/reference_markers.fasta -out GCA_017559615.1_ASM1755961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:35,643] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:35,648] [INFO] Selected 21 target genomes.
[2023-06-28 18:41:35,648] [INFO] Target genome list was writen to GCA_017559615.1_ASM1755961v1_genomic.fna/target_genomes.txt
[2023-06-28 18:41:35,656] [INFO] Task started: fastANI
[2023-06-28 18:41:35,656] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8bc4b97-54b3-4f6a-a079-231721c2a40a/GCA_017559615.1_ASM1755961v1_genomic.fna.gz --refList GCA_017559615.1_ASM1755961v1_genomic.fna/target_genomes.txt --output GCA_017559615.1_ASM1755961v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:46,310] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:46,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:46,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:46,314] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:46,314] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:41:46,314] [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
--------------------------------------------------------------------------------
[2023-06-28 18:41:46,319] [INFO] DFAST Taxonomy check result was written to GCA_017559615.1_ASM1755961v1_genomic.fna/tc_result.tsv
[2023-06-28 18:41:46,320] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:46,320] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:46,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference/checkm_data
[2023-06-28 18:41:46,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:46,352] [INFO] Task started: CheckM
[2023-06-28 18:41:46,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017559615.1_ASM1755961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017559615.1_ASM1755961v1_genomic.fna/checkm_input GCA_017559615.1_ASM1755961v1_genomic.fna/checkm_result
[2023-06-28 18:42:19,741] [INFO] Task succeeded: CheckM
[2023-06-28 18:42:19,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 18:42:19,773] [INFO] ===== Completeness check finished =====
[2023-06-28 18:42:19,773] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:42:19,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017559615.1_ASM1755961v1_genomic.fna/markers.fasta)
[2023-06-28 18:42:19,774] [INFO] Task started: Blastn
[2023-06-28 18:42:19,774] [INFO] Running command: blastn -query GCA_017559615.1_ASM1755961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67276168-30a3-47f4-8a66-b23dfaee3bd5/dqc_reference/reference_markers_gtdb.fasta -out GCA_017559615.1_ASM1755961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:42:20,583] [INFO] Task succeeded: Blastn
[2023-06-28 18:42:20,588] [INFO] Selected 8 target genomes.
[2023-06-28 18:42:20,589] [INFO] Target genome list was writen to GCA_017559615.1_ASM1755961v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:42:20,593] [INFO] Task started: fastANI
[2023-06-28 18:42:20,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8bc4b97-54b3-4f6a-a079-231721c2a40a/GCA_017559615.1_ASM1755961v1_genomic.fna.gz --refList GCA_017559615.1_ASM1755961v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017559615.1_ASM1755961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:42:23,908] [INFO] Task succeeded: fastANI
[2023-06-28 18:42:23,921] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:42:23,921] [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_017559615.1	s__Alistipes sp017559615	100.0	581	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	95.64	95.64	0.85	0.85	3	conclusive
GCA_017630455.1	s__Alistipes sp017630455	84.411	396	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017630735.1	s__Alistipes sp017630735	83.3188	347	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017380955.1	s__Alistipes sp017380955	83.0374	304	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017629985.1	s__Alistipes sp017629985	81.5375	344	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.96	97.90	0.91	0.90	3	-
GCA_017647625.1	s__Alistipes sp017647625	81.019	286	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.38	98.38	0.79	0.79	2	-
GCA_900768015.1	s__Alistipes sp900768015	79.7244	292	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	95.92	95.92	0.89	0.89	2	-
GCA_017646785.1	s__Alistipes sp017646785	79.4484	222	589	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:42:23,923] [INFO] GTDB search result was written to GCA_017559615.1_ASM1755961v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:42:23,924] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:42:23,926] [INFO] DFAST_QC result json was written to GCA_017559615.1_ASM1755961v1_genomic.fna/dqc_result.json
[2023-06-28 18:42:23,927] [INFO] DFAST_QC completed!
[2023-06-28 18:42:23,927] [INFO] Total running time: 0h1m1s