[2023-06-29 20:10:38,194] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:10:38,197] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:10:38,198] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference
[2023-06-29 20:10:40,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:10:40,558] [INFO] Task started: Prodigal
[2023-06-29 20:10:40,559] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5d450d6-98e2-41dc-be22-678b35780828/GCA_007281295.1_ASM728129v1_genomic.fna.gz | prodigal -d GCA_007281295.1_ASM728129v1_genomic.fna/cds.fna -a GCA_007281295.1_ASM728129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:10:41,717] [INFO] Task succeeded: Prodigal
[2023-06-29 20:10:41,717] [INFO] Task started: HMMsearch
[2023-06-29 20:10:41,717] [INFO] Running command: hmmsearch --tblout GCA_007281295.1_ASM728129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference/reference_markers.hmm GCA_007281295.1_ASM728129v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:10:41,936] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:10:41,938] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd5d450d6-98e2-41dc-be22-678b35780828/GCA_007281295.1_ASM728129v1_genomic.fna.gz]
[2023-06-29 20:10:41,952] [INFO] Query marker FASTA was written to GCA_007281295.1_ASM728129v1_genomic.fna/markers.fasta
[2023-06-29 20:10:41,952] [INFO] Task started: Blastn
[2023-06-29 20:10:41,952] [INFO] Running command: blastn -query GCA_007281295.1_ASM728129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference/reference_markers.fasta -out GCA_007281295.1_ASM728129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:10:45,480] [INFO] Task succeeded: Blastn
[2023-06-29 20:10:45,485] [INFO] Selected 10 target genomes.
[2023-06-29 20:10:45,485] [INFO] Target genome list was writen to GCA_007281295.1_ASM728129v1_genomic.fna/target_genomes.txt
[2023-06-29 20:10:45,527] [INFO] Task started: fastANI
[2023-06-29 20:10:45,528] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d450d6-98e2-41dc-be22-678b35780828/GCA_007281295.1_ASM728129v1_genomic.fna.gz --refList GCA_007281295.1_ASM728129v1_genomic.fna/target_genomes.txt --output GCA_007281295.1_ASM728129v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:10:51,042] [INFO] Task succeeded: fastANI
[2023-06-29 20:10:51,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:10:51,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:10:51,046] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:10:51,046] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 20:10:51,046] [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 20:10:51,048] [INFO] DFAST Taxonomy check result was written to GCA_007281295.1_ASM728129v1_genomic.fna/tc_result.tsv
[2023-06-29 20:10:51,049] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:10:51,049] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:10:51,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference/checkm_data
[2023-06-29 20:10:51,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:10:51,067] [INFO] Task started: CheckM
[2023-06-29 20:10:51,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007281295.1_ASM728129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007281295.1_ASM728129v1_genomic.fna/checkm_input GCA_007281295.1_ASM728129v1_genomic.fna/checkm_result
[2023-06-29 20:11:05,513] [INFO] Task succeeded: CheckM
[2023-06-29 20:11:05,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:11:05,533] [INFO] ===== Completeness check finished =====
[2023-06-29 20:11:05,534] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:11:05,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007281295.1_ASM728129v1_genomic.fna/markers.fasta)
[2023-06-29 20:11:05,535] [INFO] Task started: Blastn
[2023-06-29 20:11:05,535] [INFO] Running command: blastn -query GCA_007281295.1_ASM728129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb0777c5-128d-4f07-88c7-967fd3afe168/dqc_reference/reference_markers_gtdb.fasta -out GCA_007281295.1_ASM728129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:11:06,319] [INFO] Task succeeded: Blastn
[2023-06-29 20:11:06,324] [INFO] Selected 6 target genomes.
[2023-06-29 20:11:06,325] [INFO] Target genome list was writen to GCA_007281295.1_ASM728129v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:11:06,330] [INFO] Task started: fastANI
[2023-06-29 20:11:06,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5d450d6-98e2-41dc-be22-678b35780828/GCA_007281295.1_ASM728129v1_genomic.fna.gz --refList GCA_007281295.1_ASM728129v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007281295.1_ASM728129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:11:08,690] [INFO] Task succeeded: fastANI
[2023-06-29 20:11:08,698] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:11:08,698] [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_017882065.1	s__UBA877 sp017882065	91.2143	66	119	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873975.1	s__UBA877 sp903873975	85.2453	82	119	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829085.1	s__UBA877 sp903829085	80.5886	52	119	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:11:08,700] [INFO] GTDB search result was written to GCA_007281295.1_ASM728129v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:11:08,701] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:11:08,724] [INFO] DFAST_QC result json was written to GCA_007281295.1_ASM728129v1_genomic.fna/dqc_result.json
[2023-06-29 20:11:08,724] [INFO] DFAST_QC completed!
[2023-06-29 20:11:08,724] [INFO] Total running time: 0h0m31s