[2023-06-28 18:56:50,895] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:56:50,897] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:56:50,898] [INFO] DQC Reference Directory: /var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference
[2023-06-28 18:56:52,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:56:52,359] [INFO] Task started: Prodigal
[2023-06-28 18:56:52,359] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa8fc5f8-ec29-4b5b-9447-ac358a470284/GCA_027310705.1_ASM2731070v1_genomic.fna.gz | prodigal -d GCA_027310705.1_ASM2731070v1_genomic.fna/cds.fna -a GCA_027310705.1_ASM2731070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:57:01,283] [INFO] Task succeeded: Prodigal
[2023-06-28 18:57:01,284] [INFO] Task started: HMMsearch
[2023-06-28 18:57:01,284] [INFO] Running command: hmmsearch --tblout GCA_027310705.1_ASM2731070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference/reference_markers.hmm GCA_027310705.1_ASM2731070v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:57:01,513] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:57:01,514] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgaa8fc5f8-ec29-4b5b-9447-ac358a470284/GCA_027310705.1_ASM2731070v1_genomic.fna.gz]
[2023-06-28 18:57:01,539] [INFO] Query marker FASTA was written to GCA_027310705.1_ASM2731070v1_genomic.fna/markers.fasta
[2023-06-28 18:57:01,540] [INFO] Task started: Blastn
[2023-06-28 18:57:01,540] [INFO] Running command: blastn -query GCA_027310705.1_ASM2731070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference/reference_markers.fasta -out GCA_027310705.1_ASM2731070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:57:02,064] [INFO] Task succeeded: Blastn
[2023-06-28 18:57:02,069] [INFO] Selected 21 target genomes.
[2023-06-28 18:57:02,069] [INFO] Target genome list was writen to GCA_027310705.1_ASM2731070v1_genomic.fna/target_genomes.txt
[2023-06-28 18:57:02,070] [INFO] Task started: fastANI
[2023-06-28 18:57:02,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8fc5f8-ec29-4b5b-9447-ac358a470284/GCA_027310705.1_ASM2731070v1_genomic.fna.gz --refList GCA_027310705.1_ASM2731070v1_genomic.fna/target_genomes.txt --output GCA_027310705.1_ASM2731070v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:57:17,518] [INFO] Task succeeded: fastANI
[2023-06-28 18:57:17,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:57:17,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:57:17,522] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:57:17,522] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:57:17,522] [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 18:57:17,524] [INFO] DFAST Taxonomy check result was written to GCA_027310705.1_ASM2731070v1_genomic.fna/tc_result.tsv
[2023-06-28 18:57:17,524] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:57:17,524] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:57:17,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference/checkm_data
[2023-06-28 18:57:17,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:57:17,556] [INFO] Task started: CheckM
[2023-06-28 18:57:17,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310705.1_ASM2731070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310705.1_ASM2731070v1_genomic.fna/checkm_input GCA_027310705.1_ASM2731070v1_genomic.fna/checkm_result
[2023-06-28 18:57:48,734] [INFO] Task succeeded: CheckM
[2023-06-28 18:57:48,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:57:48,755] [INFO] ===== Completeness check finished =====
[2023-06-28 18:57:48,756] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:57:48,756] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310705.1_ASM2731070v1_genomic.fna/markers.fasta)
[2023-06-28 18:57:48,756] [INFO] Task started: Blastn
[2023-06-28 18:57:48,757] [INFO] Running command: blastn -query GCA_027310705.1_ASM2731070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga35377b6-efea-4c29-99df-4d6d17dd3b23/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310705.1_ASM2731070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:57:49,206] [INFO] Task succeeded: Blastn
[2023-06-28 18:57:49,210] [INFO] Selected 11 target genomes.
[2023-06-28 18:57:49,210] [INFO] Target genome list was writen to GCA_027310705.1_ASM2731070v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:57:49,214] [INFO] Task started: fastANI
[2023-06-28 18:57:49,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8fc5f8-ec29-4b5b-9447-ac358a470284/GCA_027310705.1_ASM2731070v1_genomic.fna.gz --refList GCA_027310705.1_ASM2731070v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310705.1_ASM2731070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:57:54,450] [INFO] Task succeeded: fastANI
[2023-06-28 18:57:54,457] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:57:54,457] [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_903870685.1	s__CAILAF01 sp903870685	85.0602	109	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
GCA_903904335.1	s__CAILAF01 sp903904335	80.032	90	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	97.62	96.62	0.83	0.78	4	-
GCA_903841915.1	s__CAILAF01 sp903841915	79.7242	64	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830285.1	s__CAILAF01 sp903830285	79.2563	88	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.59	99.53	0.91	0.89	4	-
GCA_903832075.1	s__CAILAF01 sp903832075	79.1265	61	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881425.1	s__CAILAF01 sp903881425	78.0398	64	152	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-28 18:57:54,459] [INFO] GTDB search result was written to GCA_027310705.1_ASM2731070v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:57:54,460] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:57:54,462] [INFO] DFAST_QC result json was written to GCA_027310705.1_ASM2731070v1_genomic.fna/dqc_result.json
[2023-06-28 18:57:54,463] [INFO] DFAST_QC completed!
[2023-06-28 18:57:54,463] [INFO] Total running time: 0h1m4s