[2023-06-19 08:39:06,792] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:39:06,794] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:39:06,794] [INFO] DQC Reference Directory: /var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference
[2023-06-19 08:39:08,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:39:08,047] [INFO] Task started: Prodigal
[2023-06-19 08:39:08,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d1f05f5-c31d-4830-94db-5f66545e236a/GCA_018659325.1_ASM1865932v1_genomic.fna.gz | prodigal -d GCA_018659325.1_ASM1865932v1_genomic.fna/cds.fna -a GCA_018659325.1_ASM1865932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:39:20,685] [INFO] Task succeeded: Prodigal
[2023-06-19 08:39:20,685] [INFO] Task started: HMMsearch
[2023-06-19 08:39:20,685] [INFO] Running command: hmmsearch --tblout GCA_018659325.1_ASM1865932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference/reference_markers.hmm GCA_018659325.1_ASM1865932v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:39:20,928] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:39:20,929] [INFO] Found 6/6 markers.
[2023-06-19 08:39:20,964] [INFO] Query marker FASTA was written to GCA_018659325.1_ASM1865932v1_genomic.fna/markers.fasta
[2023-06-19 08:39:20,965] [INFO] Task started: Blastn
[2023-06-19 08:39:20,965] [INFO] Running command: blastn -query GCA_018659325.1_ASM1865932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference/reference_markers.fasta -out GCA_018659325.1_ASM1865932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:39:21,529] [INFO] Task succeeded: Blastn
[2023-06-19 08:39:21,534] [INFO] Selected 24 target genomes.
[2023-06-19 08:39:21,534] [INFO] Target genome list was writen to GCA_018659325.1_ASM1865932v1_genomic.fna/target_genomes.txt
[2023-06-19 08:39:21,551] [INFO] Task started: fastANI
[2023-06-19 08:39:21,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1f05f5-c31d-4830-94db-5f66545e236a/GCA_018659325.1_ASM1865932v1_genomic.fna.gz --refList GCA_018659325.1_ASM1865932v1_genomic.fna/target_genomes.txt --output GCA_018659325.1_ASM1865932v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:39:34,963] [INFO] Task succeeded: fastANI
[2023-06-19 08:39:34,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:39:34,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:39:34,966] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:39:34,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:39:34,967] [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
--------------------------------------------------------------------------------
[2023-06-19 08:39:34,969] [INFO] DFAST Taxonomy check result was written to GCA_018659325.1_ASM1865932v1_genomic.fna/tc_result.tsv
[2023-06-19 08:39:34,972] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:39:34,972] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:39:34,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference/checkm_data
[2023-06-19 08:39:34,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:39:35,007] [INFO] Task started: CheckM
[2023-06-19 08:39:35,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018659325.1_ASM1865932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018659325.1_ASM1865932v1_genomic.fna/checkm_input GCA_018659325.1_ASM1865932v1_genomic.fna/checkm_result
[2023-06-19 08:40:17,339] [INFO] Task succeeded: CheckM
[2023-06-19 08:40:17,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:40:17,363] [INFO] ===== Completeness check finished =====
[2023-06-19 08:40:17,363] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:40:17,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018659325.1_ASM1865932v1_genomic.fna/markers.fasta)
[2023-06-19 08:40:17,364] [INFO] Task started: Blastn
[2023-06-19 08:40:17,364] [INFO] Running command: blastn -query GCA_018659325.1_ASM1865932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge74e6e5a-d01b-4523-93f3-ede0d7564548/dqc_reference/reference_markers_gtdb.fasta -out GCA_018659325.1_ASM1865932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:18,194] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:18,198] [INFO] Selected 25 target genomes.
[2023-06-19 08:40:18,198] [INFO] Target genome list was writen to GCA_018659325.1_ASM1865932v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:40:18,211] [INFO] Task started: fastANI
[2023-06-19 08:40:18,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1f05f5-c31d-4830-94db-5f66545e236a/GCA_018659325.1_ASM1865932v1_genomic.fna.gz --refList GCA_018659325.1_ASM1865932v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018659325.1_ASM1865932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:40:30,161] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:30,169] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:40:30,170] [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_018660685.1	s__SHAN690 sp009937235	99.9758	835	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.94	99.74	0.98	0.93	13	conclusive
GCA_905479105.1	s__SHAN690 sp002390775	76.348	50	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.12	98.21	0.92	0.80	5	-
GCA_002389645.1	s__SHAN690 sp002389645	76.0668	50	854	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.96	99.93	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-06-19 08:40:30,174] [INFO] GTDB search result was written to GCA_018659325.1_ASM1865932v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:40:30,174] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:40:30,177] [INFO] DFAST_QC result json was written to GCA_018659325.1_ASM1865932v1_genomic.fna/dqc_result.json
[2023-06-19 08:40:30,177] [INFO] DFAST_QC completed!
[2023-06-19 08:40:30,177] [INFO] Total running time: 0h1m23s