[2023-06-29 05:14:10,464] [INFO] DFAST_QC pipeline started.
[2023-06-29 05:14:10,489] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 05:14:10,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference
[2023-06-29 05:14:11,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 05:14:11,871] [INFO] Task started: Prodigal
[2023-06-29 05:14:11,871] [INFO] Running command: gunzip -c /var/lib/cwl/stge33159c7-c301-41c6-be65-bb6c38a8e4f5/GCA_012269595.1_ASM1226959v1_genomic.fna.gz | prodigal -d GCA_012269595.1_ASM1226959v1_genomic.fna/cds.fna -a GCA_012269595.1_ASM1226959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 05:14:20,632] [INFO] Task succeeded: Prodigal
[2023-06-29 05:14:20,632] [INFO] Task started: HMMsearch
[2023-06-29 05:14:20,633] [INFO] Running command: hmmsearch --tblout GCA_012269595.1_ASM1226959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference/reference_markers.hmm GCA_012269595.1_ASM1226959v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 05:14:20,886] [INFO] Task succeeded: HMMsearch
[2023-06-29 05:14:20,888] [INFO] Found 6/6 markers.
[2023-06-29 05:14:20,921] [INFO] Query marker FASTA was written to GCA_012269595.1_ASM1226959v1_genomic.fna/markers.fasta
[2023-06-29 05:14:20,922] [INFO] Task started: Blastn
[2023-06-29 05:14:20,922] [INFO] Running command: blastn -query GCA_012269595.1_ASM1226959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference/reference_markers.fasta -out GCA_012269595.1_ASM1226959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:14:21,505] [INFO] Task succeeded: Blastn
[2023-06-29 05:14:21,509] [INFO] Selected 20 target genomes.
[2023-06-29 05:14:21,510] [INFO] Target genome list was writen to GCA_012269595.1_ASM1226959v1_genomic.fna/target_genomes.txt
[2023-06-29 05:14:21,520] [INFO] Task started: fastANI
[2023-06-29 05:14:21,521] [INFO] Running command: fastANI --query /var/lib/cwl/stge33159c7-c301-41c6-be65-bb6c38a8e4f5/GCA_012269595.1_ASM1226959v1_genomic.fna.gz --refList GCA_012269595.1_ASM1226959v1_genomic.fna/target_genomes.txt --output GCA_012269595.1_ASM1226959v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 05:14:39,396] [INFO] Task succeeded: fastANI
[2023-06-29 05:14:39,397] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 05:14:39,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 05:14:39,399] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 05:14:39,400] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 05:14:39,400] [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 05:14:39,402] [INFO] DFAST Taxonomy check result was written to GCA_012269595.1_ASM1226959v1_genomic.fna/tc_result.tsv
[2023-06-29 05:14:39,403] [INFO] ===== Taxonomy check completed =====
[2023-06-29 05:14:39,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 05:14:39,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference/checkm_data
[2023-06-29 05:14:39,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 05:14:39,452] [INFO] Task started: CheckM
[2023-06-29 05:14:39,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012269595.1_ASM1226959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012269595.1_ASM1226959v1_genomic.fna/checkm_input GCA_012269595.1_ASM1226959v1_genomic.fna/checkm_result
[2023-06-29 05:15:11,565] [INFO] Task succeeded: CheckM
[2023-06-29 05:15:11,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 05:15:11,586] [INFO] ===== Completeness check finished =====
[2023-06-29 05:15:11,587] [INFO] ===== Start GTDB Search =====
[2023-06-29 05:15:11,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012269595.1_ASM1226959v1_genomic.fna/markers.fasta)
[2023-06-29 05:15:11,588] [INFO] Task started: Blastn
[2023-06-29 05:15:11,588] [INFO] Running command: blastn -query GCA_012269595.1_ASM1226959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08f73c42-49ba-4a47-b7f1-e99894cf4c6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_012269595.1_ASM1226959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 05:15:12,411] [INFO] Task succeeded: Blastn
[2023-06-29 05:15:12,416] [INFO] Selected 12 target genomes.
[2023-06-29 05:15:12,416] [INFO] Target genome list was writen to GCA_012269595.1_ASM1226959v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 05:15:12,450] [INFO] Task started: fastANI
[2023-06-29 05:15:12,451] [INFO] Running command: fastANI --query /var/lib/cwl/stge33159c7-c301-41c6-be65-bb6c38a8e4f5/GCA_012269595.1_ASM1226959v1_genomic.fna.gz --refList GCA_012269595.1_ASM1226959v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012269595.1_ASM1226959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 05:15:19,419] [INFO] Task succeeded: fastANI
[2023-06-29 05:15:19,430] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 05:15:19,430] [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_012269595.1	s__UBA12191 sp012269595	99.9999	911	914	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	99.68	99.68	0.96	0.96	2	conclusive
GCA_013911165.1	s__UBA12191 sp013911165	94.421	777	914	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691835.1	s__UBA12191 sp002691835	80.7905	259	914	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	100.00	100.00	0.93	0.93	2	-
GCA_002167285.1	s__UBA12191 sp002167285	79.9101	313	914	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__UBA12191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018694835.1	s__QNYK01 sp018694835	77.018	95	914	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.80	99.78	0.93	0.92	8	-
GCA_012960845.1	s__QNYK01 sp012960845	76.5293	96	914	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA1146;f__UBA1146;g__QNYK01	95.0	99.73	99.73	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-29 05:15:19,432] [INFO] GTDB search result was written to GCA_012269595.1_ASM1226959v1_genomic.fna/result_gtdb.tsv
[2023-06-29 05:15:19,433] [INFO] ===== GTDB Search completed =====
[2023-06-29 05:15:19,437] [INFO] DFAST_QC result json was written to GCA_012269595.1_ASM1226959v1_genomic.fna/dqc_result.json
[2023-06-29 05:15:19,437] [INFO] DFAST_QC completed!
[2023-06-29 05:15:19,437] [INFO] Total running time: 0h1m9s