[2023-06-18 17:51:27,256] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:51:27,303] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:51:27,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference
[2023-06-18 17:51:28,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:51:28,609] [INFO] Task started: Prodigal
[2023-06-18 17:51:28,609] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bd9a936-2f47-4ccf-9ea8-980d00026872/GCA_018673355.1_ASM1867335v1_genomic.fna.gz | prodigal -d GCA_018673355.1_ASM1867335v1_genomic.fna/cds.fna -a GCA_018673355.1_ASM1867335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:51:48,598] [INFO] Task succeeded: Prodigal
[2023-06-18 17:51:48,599] [INFO] Task started: HMMsearch
[2023-06-18 17:51:48,599] [INFO] Running command: hmmsearch --tblout GCA_018673355.1_ASM1867335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference/reference_markers.hmm GCA_018673355.1_ASM1867335v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:51:48,875] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:51:48,876] [INFO] Found 6/6 markers.
[2023-06-18 17:51:48,915] [INFO] Query marker FASTA was written to GCA_018673355.1_ASM1867335v1_genomic.fna/markers.fasta
[2023-06-18 17:51:48,915] [INFO] Task started: Blastn
[2023-06-18 17:51:48,916] [INFO] Running command: blastn -query GCA_018673355.1_ASM1867335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference/reference_markers.fasta -out GCA_018673355.1_ASM1867335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:51:49,564] [INFO] Task succeeded: Blastn
[2023-06-18 17:51:49,568] [INFO] Selected 21 target genomes.
[2023-06-18 17:51:49,569] [INFO] Target genome list was writen to GCA_018673355.1_ASM1867335v1_genomic.fna/target_genomes.txt
[2023-06-18 17:51:49,579] [INFO] Task started: fastANI
[2023-06-18 17:51:49,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd9a936-2f47-4ccf-9ea8-980d00026872/GCA_018673355.1_ASM1867335v1_genomic.fna.gz --refList GCA_018673355.1_ASM1867335v1_genomic.fna/target_genomes.txt --output GCA_018673355.1_ASM1867335v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:52:04,877] [INFO] Task succeeded: fastANI
[2023-06-18 17:52:04,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:52:04,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:52:04,880] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:52:04,880] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:52:04,881] [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
--------------------------------------------------------------------------------
[2023-06-18 17:52:04,886] [INFO] DFAST Taxonomy check result was written to GCA_018673355.1_ASM1867335v1_genomic.fna/tc_result.tsv
[2023-06-18 17:52:04,888] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:52:04,889] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:52:04,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference/checkm_data
[2023-06-18 17:52:04,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:52:04,932] [INFO] Task started: CheckM
[2023-06-18 17:52:04,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018673355.1_ASM1867335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018673355.1_ASM1867335v1_genomic.fna/checkm_input GCA_018673355.1_ASM1867335v1_genomic.fna/checkm_result
[2023-06-18 17:53:00,382] [INFO] Task succeeded: CheckM
[2023-06-18 17:53:00,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:53:00,409] [INFO] ===== Completeness check finished =====
[2023-06-18 17:53:00,410] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:53:00,410] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018673355.1_ASM1867335v1_genomic.fna/markers.fasta)
[2023-06-18 17:53:00,410] [INFO] Task started: Blastn
[2023-06-18 17:53:00,411] [INFO] Running command: blastn -query GCA_018673355.1_ASM1867335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d623b6c-f2ac-4ef0-8319-d51b05c8c770/dqc_reference/reference_markers_gtdb.fasta -out GCA_018673355.1_ASM1867335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:53:01,286] [INFO] Task succeeded: Blastn
[2023-06-18 17:53:01,296] [INFO] Selected 7 target genomes.
[2023-06-18 17:53:01,296] [INFO] Target genome list was writen to GCA_018673355.1_ASM1867335v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:53:01,302] [INFO] Task started: fastANI
[2023-06-18 17:53:01,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bd9a936-2f47-4ccf-9ea8-980d00026872/GCA_018673355.1_ASM1867335v1_genomic.fna.gz --refList GCA_018673355.1_ASM1867335v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018673355.1_ASM1867335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:53:05,655] [INFO] Task succeeded: fastANI
[2023-06-18 17:53:05,668] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:53:05,668] [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_018674955.1	s__UBA1096 sp018674955	98.8878	660	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.88	98.74	0.86	0.81	14	conclusive
GCA_015658765.1	s__UBA1096 sp015658765	90.6694	393	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002299785.1	s__UBA1096 sp002299785	88.8273	435	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972865.1	s__UBA1096 sp003972865	86.2285	451	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	84.1473	610	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	82.5117	526	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453165.1	s__UBA1096 sp002453165	78.377	297	765	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
--------------------------------------------------------------------------------
[2023-06-18 17:53:05,676] [INFO] GTDB search result was written to GCA_018673355.1_ASM1867335v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:53:05,676] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:53:05,679] [INFO] DFAST_QC result json was written to GCA_018673355.1_ASM1867335v1_genomic.fna/dqc_result.json
[2023-06-18 17:53:05,679] [INFO] DFAST_QC completed!
[2023-06-18 17:53:05,680] [INFO] Total running time: 0h1m38s