[2023-06-19 00:40:15,202] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:40:15,205] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:40:15,206] [INFO] DQC Reference Directory: /var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference
[2023-06-19 00:40:16,541] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:40:16,542] [INFO] Task started: Prodigal
[2023-06-19 00:40:16,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg47e65710-74c5-48dc-91f3-05f97679f2f8/GCA_018780035.1_ASM1878003v1_genomic.fna.gz | prodigal -d GCA_018780035.1_ASM1878003v1_genomic.fna/cds.fna -a GCA_018780035.1_ASM1878003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:40:36,200] [INFO] Task succeeded: Prodigal
[2023-06-19 00:40:36,200] [INFO] Task started: HMMsearch
[2023-06-19 00:40:36,201] [INFO] Running command: hmmsearch --tblout GCA_018780035.1_ASM1878003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference/reference_markers.hmm GCA_018780035.1_ASM1878003v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:40:36,572] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:40:36,577] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg47e65710-74c5-48dc-91f3-05f97679f2f8/GCA_018780035.1_ASM1878003v1_genomic.fna.gz]
[2023-06-19 00:40:36,640] [INFO] Query marker FASTA was written to GCA_018780035.1_ASM1878003v1_genomic.fna/markers.fasta
[2023-06-19 00:40:36,641] [INFO] Task started: Blastn
[2023-06-19 00:40:36,641] [INFO] Running command: blastn -query GCA_018780035.1_ASM1878003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference/reference_markers.fasta -out GCA_018780035.1_ASM1878003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:40:37,290] [INFO] Task succeeded: Blastn
[2023-06-19 00:40:37,298] [INFO] Selected 17 target genomes.
[2023-06-19 00:40:37,299] [INFO] Target genome list was writen to GCA_018780035.1_ASM1878003v1_genomic.fna/target_genomes.txt
[2023-06-19 00:40:37,303] [INFO] Task started: fastANI
[2023-06-19 00:40:37,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e65710-74c5-48dc-91f3-05f97679f2f8/GCA_018780035.1_ASM1878003v1_genomic.fna.gz --refList GCA_018780035.1_ASM1878003v1_genomic.fna/target_genomes.txt --output GCA_018780035.1_ASM1878003v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:40:48,558] [INFO] Task succeeded: fastANI
[2023-06-19 00:40:48,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:40:48,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:40:48,563] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:40:48,563] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:40:48,563] [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
--------------------------------------------------------------------------------
[2023-06-19 00:40:48,565] [INFO] DFAST Taxonomy check result was written to GCA_018780035.1_ASM1878003v1_genomic.fna/tc_result.tsv
[2023-06-19 00:40:48,566] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:40:48,566] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:40:48,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference/checkm_data
[2023-06-19 00:40:48,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:40:48,637] [INFO] Task started: CheckM
[2023-06-19 00:40:48,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018780035.1_ASM1878003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018780035.1_ASM1878003v1_genomic.fna/checkm_input GCA_018780035.1_ASM1878003v1_genomic.fna/checkm_result
[2023-06-19 00:41:46,719] [INFO] Task succeeded: CheckM
[2023-06-19 00:41:46,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:41:46,751] [INFO] ===== Completeness check finished =====
[2023-06-19 00:41:46,752] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:41:46,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018780035.1_ASM1878003v1_genomic.fna/markers.fasta)
[2023-06-19 00:41:46,752] [INFO] Task started: Blastn
[2023-06-19 00:41:46,752] [INFO] Running command: blastn -query GCA_018780035.1_ASM1878003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64812685-1814-49e3-99f3-63633fab6794/dqc_reference/reference_markers_gtdb.fasta -out GCA_018780035.1_ASM1878003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:41:47,717] [INFO] Task succeeded: Blastn
[2023-06-19 00:41:47,723] [INFO] Selected 17 target genomes.
[2023-06-19 00:41:47,723] [INFO] Target genome list was writen to GCA_018780035.1_ASM1878003v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:41:47,854] [INFO] Task started: fastANI
[2023-06-19 00:41:47,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg47e65710-74c5-48dc-91f3-05f97679f2f8/GCA_018780035.1_ASM1878003v1_genomic.fna.gz --refList GCA_018780035.1_ASM1878003v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018780035.1_ASM1878003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:41:59,769] [INFO] Task succeeded: fastANI
[2023-06-19 00:41:59,778] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:41:59,779] [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_018780035.1	s__GCA-2770975 sp018780035	100.0	2118	2123	d__Bacteria;p__Cyanobacteria;c__Sericytochromatia;o__UBA7694;f__UBA7694;g__GCA-2770975	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002783405.1	s__GCA-2770975 sp002783405	77.47	467	2123	d__Bacteria;p__Cyanobacteria;c__Sericytochromatia;o__UBA7694;f__UBA7694;g__GCA-2770975	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002482705.1	s__UBA7694 sp002482705	76.3146	82	2123	d__Bacteria;p__Cyanobacteria;c__Sericytochromatia;o__UBA7694;f__UBA7694;g__UBA7694	95.0	100.00	100.00	0.96	0.96	2	-
GCA_015272195.1	s__JACYMC01 sp015272195	76.0841	133	2123	d__Bacteria;p__Cyanobacteria;c__Sericytochromatia;o__UBA7694;f__UBA7694;g__JACYMC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:41:59,781] [INFO] GTDB search result was written to GCA_018780035.1_ASM1878003v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:41:59,782] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:41:59,787] [INFO] DFAST_QC result json was written to GCA_018780035.1_ASM1878003v1_genomic.fna/dqc_result.json
[2023-06-19 00:41:59,788] [INFO] DFAST_QC completed!
[2023-06-19 00:41:59,788] [INFO] Total running time: 0h1m45s