[2023-06-19 12:10:32,770] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:32,773] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:32,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference
[2023-06-19 12:10:34,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:34,083] [INFO] Task started: Prodigal
[2023-06-19 12:10:34,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgab96bf64-7136-42e7-8c1c-f72d5cd549c5/GCA_018894875.1_ASM1889487v1_genomic.fna.gz | prodigal -d GCA_018894875.1_ASM1889487v1_genomic.fna/cds.fna -a GCA_018894875.1_ASM1889487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:36,576] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:36,577] [INFO] Task started: HMMsearch
[2023-06-19 12:10:36,577] [INFO] Running command: hmmsearch --tblout GCA_018894875.1_ASM1889487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference/reference_markers.hmm GCA_018894875.1_ASM1889487v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:36,919] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:36,921] [INFO] Found 6/6 markers.
[2023-06-19 12:10:36,950] [INFO] Query marker FASTA was written to GCA_018894875.1_ASM1889487v1_genomic.fna/markers.fasta
[2023-06-19 12:10:36,951] [INFO] Task started: Blastn
[2023-06-19 12:10:36,951] [INFO] Running command: blastn -query GCA_018894875.1_ASM1889487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference/reference_markers.fasta -out GCA_018894875.1_ASM1889487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:39,829] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:39,834] [INFO] Selected 9 target genomes.
[2023-06-19 12:10:39,834] [INFO] Target genome list was writen to GCA_018894875.1_ASM1889487v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:39,861] [INFO] Task started: fastANI
[2023-06-19 12:10:39,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgab96bf64-7136-42e7-8c1c-f72d5cd549c5/GCA_018894875.1_ASM1889487v1_genomic.fna.gz --refList GCA_018894875.1_ASM1889487v1_genomic.fna/target_genomes.txt --output GCA_018894875.1_ASM1889487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:10:45,139] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:45,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:10:45,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:10:45,142] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:10:45,142] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:10:45,142] [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 12:10:45,144] [INFO] DFAST Taxonomy check result was written to GCA_018894875.1_ASM1889487v1_genomic.fna/tc_result.tsv
[2023-06-19 12:10:45,145] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:10:45,145] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:45,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference/checkm_data
[2023-06-19 12:10:45,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:45,167] [INFO] Task started: CheckM
[2023-06-19 12:10:45,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018894875.1_ASM1889487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018894875.1_ASM1889487v1_genomic.fna/checkm_input GCA_018894875.1_ASM1889487v1_genomic.fna/checkm_result
[2023-06-19 12:11:01,052] [INFO] Task succeeded: CheckM
[2023-06-19 12:11:01,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:11:01,073] [INFO] ===== Completeness check finished =====
[2023-06-19 12:11:01,073] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:11:01,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018894875.1_ASM1889487v1_genomic.fna/markers.fasta)
[2023-06-19 12:11:01,074] [INFO] Task started: Blastn
[2023-06-19 12:11:01,074] [INFO] Running command: blastn -query GCA_018894875.1_ASM1889487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e666622-ded0-43d3-894d-48508618d713/dqc_reference/reference_markers_gtdb.fasta -out GCA_018894875.1_ASM1889487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:11:01,911] [INFO] Task succeeded: Blastn
[2023-06-19 12:11:01,915] [INFO] Selected 17 target genomes.
[2023-06-19 12:11:01,915] [INFO] Target genome list was writen to GCA_018894875.1_ASM1889487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:11:01,922] [INFO] Task started: fastANI
[2023-06-19 12:11:01,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgab96bf64-7136-42e7-8c1c-f72d5cd549c5/GCA_018894875.1_ASM1889487v1_genomic.fna.gz --refList GCA_018894875.1_ASM1889487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018894875.1_ASM1889487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:11:06,543] [INFO] Task succeeded: fastANI
[2023-06-19 12:11:06,553] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:11:06,554] [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_018896815.1	s__JAHILY01 sp018896815	99.6726	292	346	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHILY01	95.0	99.67	99.67	0.84	0.84	2	conclusive
GCA_018902915.1	s__JAHIPS01 sp018902915	77.4643	104	346	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHIPS01	95.0	99.40	99.40	0.74	0.74	2	-
GCA_013202925.1	s__JABMRA01 sp013202925	77.4478	70	346	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JABMRA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018818505.1	s__JAHIRR01 sp018818505	77.0903	76	346	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10183;f__UBA10183;g__JAHIRR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:11:06,556] [INFO] GTDB search result was written to GCA_018894875.1_ASM1889487v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:11:06,556] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:11:06,559] [INFO] DFAST_QC result json was written to GCA_018894875.1_ASM1889487v1_genomic.fna/dqc_result.json
[2023-06-19 12:11:06,559] [INFO] DFAST_QC completed!
[2023-06-19 12:11:06,559] [INFO] Total running time: 0h0m34s