[2023-06-13 19:15:31,955] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:15:31,957] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:15:31,957] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference
[2023-06-13 19:15:33,069] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:15:33,070] [INFO] Task started: Prodigal
[2023-06-13 19:15:33,070] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e47927b-a58b-433f-b162-1537cfe2ed33/GCA_022708305.1_ASM2270830v1_genomic.fna.gz | prodigal -d GCA_022708305.1_ASM2270830v1_genomic.fna/cds.fna -a GCA_022708305.1_ASM2270830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:15:40,997] [INFO] Task succeeded: Prodigal
[2023-06-13 19:15:40,998] [INFO] Task started: HMMsearch
[2023-06-13 19:15:40,998] [INFO] Running command: hmmsearch --tblout GCA_022708305.1_ASM2270830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference/reference_markers.hmm GCA_022708305.1_ASM2270830v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:15:41,190] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:15:41,191] [INFO] Found 6/6 markers.
[2023-06-13 19:15:41,210] [INFO] Query marker FASTA was written to GCA_022708305.1_ASM2270830v1_genomic.fna/markers.fasta
[2023-06-13 19:15:41,211] [INFO] Task started: Blastn
[2023-06-13 19:15:41,211] [INFO] Running command: blastn -query GCA_022708305.1_ASM2270830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference/reference_markers.fasta -out GCA_022708305.1_ASM2270830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:15:41,736] [INFO] Task succeeded: Blastn
[2023-06-13 19:15:41,740] [INFO] Selected 28 target genomes.
[2023-06-13 19:15:41,740] [INFO] Target genome list was writen to GCA_022708305.1_ASM2270830v1_genomic.fna/target_genomes.txt
[2023-06-13 19:15:41,742] [INFO] Task started: fastANI
[2023-06-13 19:15:41,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e47927b-a58b-433f-b162-1537cfe2ed33/GCA_022708305.1_ASM2270830v1_genomic.fna.gz --refList GCA_022708305.1_ASM2270830v1_genomic.fna/target_genomes.txt --output GCA_022708305.1_ASM2270830v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:16:01,399] [INFO] Task succeeded: fastANI
[2023-06-13 19:16:01,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:16:01,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:16:01,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:16:01,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 19:16:01,402] [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
--------------------------------------------------------------------------------
[2023-06-13 19:16:01,408] [INFO] DFAST Taxonomy check result was written to GCA_022708305.1_ASM2270830v1_genomic.fna/tc_result.tsv
[2023-06-13 19:16:01,409] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:16:01,409] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:16:01,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference/checkm_data
[2023-06-13 19:16:01,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:16:01,435] [INFO] Task started: CheckM
[2023-06-13 19:16:01,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708305.1_ASM2270830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708305.1_ASM2270830v1_genomic.fna/checkm_input GCA_022708305.1_ASM2270830v1_genomic.fna/checkm_result
[2023-06-13 19:16:28,659] [INFO] Task succeeded: CheckM
[2023-06-13 19:16:28,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 19:16:28,681] [INFO] ===== Completeness check finished =====
[2023-06-13 19:16:28,681] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:16:28,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708305.1_ASM2270830v1_genomic.fna/markers.fasta)
[2023-06-13 19:16:28,683] [INFO] Task started: Blastn
[2023-06-13 19:16:28,683] [INFO] Running command: blastn -query GCA_022708305.1_ASM2270830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb0e7713-cd6d-4083-98d2-bf27f6ab236d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708305.1_ASM2270830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:16:29,423] [INFO] Task succeeded: Blastn
[2023-06-13 19:16:29,427] [INFO] Selected 10 target genomes.
[2023-06-13 19:16:29,427] [INFO] Target genome list was writen to GCA_022708305.1_ASM2270830v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:16:29,432] [INFO] Task started: fastANI
[2023-06-13 19:16:29,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e47927b-a58b-433f-b162-1537cfe2ed33/GCA_022708305.1_ASM2270830v1_genomic.fna.gz --refList GCA_022708305.1_ASM2270830v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708305.1_ASM2270830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:16:33,220] [INFO] Task succeeded: fastANI
[2023-06-13 19:16:33,226] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:16:33,226] [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_017992915.1	s__Bact-11 sp017992915	98.7087	311	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002376715.1	s__Bact-11 sp002376715	92.5805	463	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012511975.1	s__Bact-11 sp012511975	85.9111	344	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728975.1	s__Bact-11 sp012728975	85.5014	447	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305275.1	s__Bact-11 sp002305275	83.9637	469	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798805.1	s__Bact-11 sp012798805	82.0819	388	604	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:16:33,228] [INFO] GTDB search result was written to GCA_022708305.1_ASM2270830v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:16:33,228] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:16:33,231] [INFO] DFAST_QC result json was written to GCA_022708305.1_ASM2270830v1_genomic.fna/dqc_result.json
[2023-06-13 19:16:33,231] [INFO] DFAST_QC completed!
[2023-06-13 19:16:33,231] [INFO] Total running time: 0h1m1s