[2023-06-29 17:08:37,308] [INFO] DFAST_QC pipeline started.
[2023-06-29 17:08:37,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 17:08:37,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference
[2023-06-29 17:08:38,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 17:08:38,962] [INFO] Task started: Prodigal
[2023-06-29 17:08:38,962] [INFO] Running command: gunzip -c /var/lib/cwl/stga815092a-07f7-4cc0-a61b-838d16e10b9a/GCA_021633065.1_ASM2163306v1_genomic.fna.gz | prodigal -d GCA_021633065.1_ASM2163306v1_genomic.fna/cds.fna -a GCA_021633065.1_ASM2163306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 17:08:41,760] [INFO] Task succeeded: Prodigal
[2023-06-29 17:08:41,760] [INFO] Task started: HMMsearch
[2023-06-29 17:08:41,760] [INFO] Running command: hmmsearch --tblout GCA_021633065.1_ASM2163306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference/reference_markers.hmm GCA_021633065.1_ASM2163306v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 17:08:42,023] [INFO] Task succeeded: HMMsearch
[2023-06-29 17:08:42,024] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga815092a-07f7-4cc0-a61b-838d16e10b9a/GCA_021633065.1_ASM2163306v1_genomic.fna.gz]
[2023-06-29 17:08:42,093] [INFO] Query marker FASTA was written to GCA_021633065.1_ASM2163306v1_genomic.fna/markers.fasta
[2023-06-29 17:08:42,093] [INFO] Task started: Blastn
[2023-06-29 17:08:42,094] [INFO] Running command: blastn -query GCA_021633065.1_ASM2163306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference/reference_markers.fasta -out GCA_021633065.1_ASM2163306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:08:42,740] [INFO] Task succeeded: Blastn
[2023-06-29 17:08:42,744] [INFO] Selected 13 target genomes.
[2023-06-29 17:08:42,745] [INFO] Target genome list was writen to GCA_021633065.1_ASM2163306v1_genomic.fna/target_genomes.txt
[2023-06-29 17:08:42,748] [INFO] Task started: fastANI
[2023-06-29 17:08:42,748] [INFO] Running command: fastANI --query /var/lib/cwl/stga815092a-07f7-4cc0-a61b-838d16e10b9a/GCA_021633065.1_ASM2163306v1_genomic.fna.gz --refList GCA_021633065.1_ASM2163306v1_genomic.fna/target_genomes.txt --output GCA_021633065.1_ASM2163306v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 17:08:47,368] [INFO] Task succeeded: fastANI
[2023-06-29 17:08:47,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 17:08:47,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 17:08:47,370] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 17:08:47,370] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 17:08:47,370] [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
--------------------------------------------------------------------------------
[2023-06-29 17:08:47,372] [INFO] DFAST Taxonomy check result was written to GCA_021633065.1_ASM2163306v1_genomic.fna/tc_result.tsv
[2023-06-29 17:08:47,373] [INFO] ===== Taxonomy check completed =====
[2023-06-29 17:08:47,373] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 17:08:47,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference/checkm_data
[2023-06-29 17:08:47,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 17:08:47,398] [INFO] Task started: CheckM
[2023-06-29 17:08:47,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021633065.1_ASM2163306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021633065.1_ASM2163306v1_genomic.fna/checkm_input GCA_021633065.1_ASM2163306v1_genomic.fna/checkm_result
[2023-06-29 17:09:04,276] [INFO] Task succeeded: CheckM
[2023-06-29 17:09:04,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 17:09:04,303] [INFO] ===== Completeness check finished =====
[2023-06-29 17:09:04,303] [INFO] ===== Start GTDB Search =====
[2023-06-29 17:09:04,303] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021633065.1_ASM2163306v1_genomic.fna/markers.fasta)
[2023-06-29 17:09:04,304] [INFO] Task started: Blastn
[2023-06-29 17:09:04,304] [INFO] Running command: blastn -query GCA_021633065.1_ASM2163306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8f0ad21-5d43-4fae-9b19-e78c4570693e/dqc_reference/reference_markers_gtdb.fasta -out GCA_021633065.1_ASM2163306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 17:09:05,187] [INFO] Task succeeded: Blastn
[2023-06-29 17:09:05,191] [INFO] Selected 15 target genomes.
[2023-06-29 17:09:05,191] [INFO] Target genome list was writen to GCA_021633065.1_ASM2163306v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 17:09:05,197] [INFO] Task started: fastANI
[2023-06-29 17:09:05,198] [INFO] Running command: fastANI --query /var/lib/cwl/stga815092a-07f7-4cc0-a61b-838d16e10b9a/GCA_021633065.1_ASM2163306v1_genomic.fna.gz --refList GCA_021633065.1_ASM2163306v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021633065.1_ASM2163306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 17:09:10,141] [INFO] Task succeeded: fastANI
[2023-06-29 17:09:10,153] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 17:09:10,153] [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_003258725.1	s__UBA6984 sp003258725	98.7408	387	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	98.56	98.53	0.92	0.92	3	conclusive
GCA_900550295.1	s__UBA6984 sp900550295	86.3153	330	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	99.30	99.12	0.94	0.93	3	-
GCA_002297005.1	s__UBA791 sp002297005	80.9418	142	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235155.1	s__UBA6984 sp905235155	78.8078	202	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450015.1	s__UBA6984 sp002450015	78.7924	153	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405375.1	s__UBA6984 sp017405375	78.7676	118	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512405.1	s__UBA6984 sp017512405	78.6092	158	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803265.1	s__UBA791 sp902803265	78.5554	78	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369055.1	s__UBA6984 sp002369055	78.4419	145	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766355.1	s__UMGS1585 sp900766355	78.3873	75	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UMGS1585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236205.1	s__UBA6984 sp905236205	78.1222	143	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA6984	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783785.1	s__UBA791 sp902783785	77.9719	90	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797985.1	s__UBA2883 sp902797985	77.4138	56	404	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2883	95.0	98.86	98.86	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-29 17:09:10,155] [INFO] GTDB search result was written to GCA_021633065.1_ASM2163306v1_genomic.fna/result_gtdb.tsv
[2023-06-29 17:09:10,155] [INFO] ===== GTDB Search completed =====
[2023-06-29 17:09:10,180] [INFO] DFAST_QC result json was written to GCA_021633065.1_ASM2163306v1_genomic.fna/dqc_result.json
[2023-06-29 17:09:10,181] [INFO] DFAST_QC completed!
[2023-06-29 17:09:10,181] [INFO] Total running time: 0h0m33s