[2023-06-19 07:30:04,726] [INFO] DFAST_QC pipeline started.
[2023-06-19 07:30:04,729] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 07:30:04,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference
[2023-06-19 07:30:05,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 07:30:05,967] [INFO] Task started: Prodigal
[2023-06-19 07:30:05,967] [INFO] Running command: gunzip -c /var/lib/cwl/stg1308dc1f-e2ef-44c4-abb8-65132544e376/GCA_018266655.1_ASM1826665v1_genomic.fna.gz | prodigal -d GCA_018266655.1_ASM1826665v1_genomic.fna/cds.fna -a GCA_018266655.1_ASM1826665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 07:30:22,219] [INFO] Task succeeded: Prodigal
[2023-06-19 07:30:22,219] [INFO] Task started: HMMsearch
[2023-06-19 07:30:22,220] [INFO] Running command: hmmsearch --tblout GCA_018266655.1_ASM1826665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference/reference_markers.hmm GCA_018266655.1_ASM1826665v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 07:30:22,556] [INFO] Task succeeded: HMMsearch
[2023-06-19 07:30:22,557] [INFO] Found 6/6 markers.
[2023-06-19 07:30:22,594] [INFO] Query marker FASTA was written to GCA_018266655.1_ASM1826665v1_genomic.fna/markers.fasta
[2023-06-19 07:30:22,594] [INFO] Task started: Blastn
[2023-06-19 07:30:22,594] [INFO] Running command: blastn -query GCA_018266655.1_ASM1826665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference/reference_markers.fasta -out GCA_018266655.1_ASM1826665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:30:23,205] [INFO] Task succeeded: Blastn
[2023-06-19 07:30:23,210] [INFO] Selected 22 target genomes.
[2023-06-19 07:30:23,210] [INFO] Target genome list was writen to GCA_018266655.1_ASM1826665v1_genomic.fna/target_genomes.txt
[2023-06-19 07:30:23,214] [INFO] Task started: fastANI
[2023-06-19 07:30:23,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg1308dc1f-e2ef-44c4-abb8-65132544e376/GCA_018266655.1_ASM1826665v1_genomic.fna.gz --refList GCA_018266655.1_ASM1826665v1_genomic.fna/target_genomes.txt --output GCA_018266655.1_ASM1826665v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 07:30:43,581] [INFO] Task succeeded: fastANI
[2023-06-19 07:30:43,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 07:30:43,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 07:30:43,591] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 07:30:43,591] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 07:30:43,592] [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
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	76.2837	53	724	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.7001	53	724	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	75.6751	74	724	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	75.6042	64	724	95	below_threshold
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	75.5778	50	724	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	75.4315	53	724	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.3726	51	724	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 07:30:43,594] [INFO] DFAST Taxonomy check result was written to GCA_018266655.1_ASM1826665v1_genomic.fna/tc_result.tsv
[2023-06-19 07:30:43,595] [INFO] ===== Taxonomy check completed =====
[2023-06-19 07:30:43,595] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 07:30:43,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference/checkm_data
[2023-06-19 07:30:43,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 07:30:43,635] [INFO] Task started: CheckM
[2023-06-19 07:30:43,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018266655.1_ASM1826665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018266655.1_ASM1826665v1_genomic.fna/checkm_input GCA_018266655.1_ASM1826665v1_genomic.fna/checkm_result
[2023-06-19 07:31:32,956] [INFO] Task succeeded: CheckM
[2023-06-19 07:31:32,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 07:31:32,978] [INFO] ===== Completeness check finished =====
[2023-06-19 07:31:32,978] [INFO] ===== Start GTDB Search =====
[2023-06-19 07:31:32,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018266655.1_ASM1826665v1_genomic.fna/markers.fasta)
[2023-06-19 07:31:32,979] [INFO] Task started: Blastn
[2023-06-19 07:31:32,979] [INFO] Running command: blastn -query GCA_018266655.1_ASM1826665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e177722-e2a9-478c-af48-60c8dd842927/dqc_reference/reference_markers_gtdb.fasta -out GCA_018266655.1_ASM1826665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 07:31:33,749] [INFO] Task succeeded: Blastn
[2023-06-19 07:31:33,754] [INFO] Selected 17 target genomes.
[2023-06-19 07:31:33,754] [INFO] Target genome list was writen to GCA_018266655.1_ASM1826665v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 07:31:33,764] [INFO] Task started: fastANI
[2023-06-19 07:31:33,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg1308dc1f-e2ef-44c4-abb8-65132544e376/GCA_018266655.1_ASM1826665v1_genomic.fna.gz --refList GCA_018266655.1_ASM1826665v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018266655.1_ASM1826665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 07:31:44,283] [INFO] Task succeeded: fastANI
[2023-06-19 07:31:44,293] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 07:31:44,293] [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_018266575.1	s__Puia sp018266575	98.8542	720	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013288945.1	s__Puia sp013288945	77.3939	167	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927975.1	s__Puia sp903927975	76.8159	167	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	99.89	99.89	0.91	0.91	2	-
GCA_018267575.1	s__Puia sp018267575	76.384	84	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267615.1	s__Puia sp018267615	76.3316	122	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028795.1	s__CW01 sp004028795	75.7004	58	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.97	99.97	0.97	0.97	2	-
GCF_007971225.1	s__Panacibacter ginsenosidivorans	75.6739	72	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115755.1	s__Parafilimonas terrae	75.6042	64	724	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 07:31:44,295] [INFO] GTDB search result was written to GCA_018266655.1_ASM1826665v1_genomic.fna/result_gtdb.tsv
[2023-06-19 07:31:44,296] [INFO] ===== GTDB Search completed =====
[2023-06-19 07:31:44,299] [INFO] DFAST_QC result json was written to GCA_018266655.1_ASM1826665v1_genomic.fna/dqc_result.json
[2023-06-19 07:31:44,299] [INFO] DFAST_QC completed!
[2023-06-19 07:31:44,299] [INFO] Total running time: 0h1m40s