[2023-06-18 13:03:32,947] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:32,950] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:32,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference
[2023-06-18 13:03:34,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:34,694] [INFO] Task started: Prodigal
[2023-06-18 13:03:34,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg092ef28c-6a96-4827-8b74-d1154ed1b6ea/GCA_018897335.1_ASM1889733v1_genomic.fna.gz | prodigal -d GCA_018897335.1_ASM1889733v1_genomic.fna/cds.fna -a GCA_018897335.1_ASM1889733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:38,381] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:38,381] [INFO] Task started: HMMsearch
[2023-06-18 13:03:38,381] [INFO] Running command: hmmsearch --tblout GCA_018897335.1_ASM1889733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference/reference_markers.hmm GCA_018897335.1_ASM1889733v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:38,574] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:38,577] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg092ef28c-6a96-4827-8b74-d1154ed1b6ea/GCA_018897335.1_ASM1889733v1_genomic.fna.gz]
[2023-06-18 13:03:38,610] [INFO] Query marker FASTA was written to GCA_018897335.1_ASM1889733v1_genomic.fna/markers.fasta
[2023-06-18 13:03:38,611] [INFO] Task started: Blastn
[2023-06-18 13:03:38,611] [INFO] Running command: blastn -query GCA_018897335.1_ASM1889733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference/reference_markers.fasta -out GCA_018897335.1_ASM1889733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:39,140] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:39,147] [INFO] Selected 15 target genomes.
[2023-06-18 13:03:39,147] [INFO] Target genome list was writen to GCA_018897335.1_ASM1889733v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:39,149] [INFO] Task started: fastANI
[2023-06-18 13:03:39,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg092ef28c-6a96-4827-8b74-d1154ed1b6ea/GCA_018897335.1_ASM1889733v1_genomic.fna.gz --refList GCA_018897335.1_ASM1889733v1_genomic.fna/target_genomes.txt --output GCA_018897335.1_ASM1889733v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:03:53,163] [INFO] Task succeeded: fastANI
[2023-06-18 13:03:53,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:03:53,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:03:53,165] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:03:53,165] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:03:53,165] [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 13:03:53,169] [INFO] DFAST Taxonomy check result was written to GCA_018897335.1_ASM1889733v1_genomic.fna/tc_result.tsv
[2023-06-18 13:03:53,169] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:03:53,170] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:03:53,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference/checkm_data
[2023-06-18 13:03:53,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:03:53,205] [INFO] Task started: CheckM
[2023-06-18 13:03:53,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018897335.1_ASM1889733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018897335.1_ASM1889733v1_genomic.fna/checkm_input GCA_018897335.1_ASM1889733v1_genomic.fna/checkm_result
[2023-06-18 13:04:11,868] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:11,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:11,903] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:11,904] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:11,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018897335.1_ASM1889733v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:11,905] [INFO] Task started: Blastn
[2023-06-18 13:04:11,905] [INFO] Running command: blastn -query GCA_018897335.1_ASM1889733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63ba952d-49f4-43ce-8939-4da0b39ba47a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018897335.1_ASM1889733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:12,416] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:12,421] [INFO] Selected 14 target genomes.
[2023-06-18 13:04:12,421] [INFO] Target genome list was writen to GCA_018897335.1_ASM1889733v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:12,470] [INFO] Task started: fastANI
[2023-06-18 13:04:12,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg092ef28c-6a96-4827-8b74-d1154ed1b6ea/GCA_018897335.1_ASM1889733v1_genomic.fna.gz --refList GCA_018897335.1_ASM1889733v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018897335.1_ASM1889733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:20,675] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:20,686] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:20,687] [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_018896395.1	s__VSJD01 sp018896395	98.385	250	314	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	98.50	98.47	0.77	0.75	3	conclusive
GCA_008636095.1	s__VSJD01 sp008636095	89.2805	231	314	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	99.74	99.73	0.88	0.86	5	-
GCA_016182435.1	s__VSJD01 sp016182435	78.5761	102	314	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016188985.1	s__VSJD01 sp016188985	77.9982	126	314	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__VSJD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018898455.1	s__JAHIJO01 sp018898455	77.0831	57	314	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__JAAZAB01;f__VSJD01;g__JAHIJO01	95.0	99.93	99.88	0.95	0.94	4	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:20,691] [INFO] GTDB search result was written to GCA_018897335.1_ASM1889733v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:20,691] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:20,696] [INFO] DFAST_QC result json was written to GCA_018897335.1_ASM1889733v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:20,696] [INFO] DFAST_QC completed!
[2023-06-18 13:04:20,696] [INFO] Total running time: 0h0m48s