[2023-06-13 16:46:33,135] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:46:33,137] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:46:33,138] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference
[2023-06-13 16:46:34,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:46:34,266] [INFO] Task started: Prodigal
[2023-06-13 16:46:34,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg2bb9ec11-3335-42ab-bca3-2e0100b458ba/GCA_022448505.1_ASM2244850v1_genomic.fna.gz | prodigal -d GCA_022448505.1_ASM2244850v1_genomic.fna/cds.fna -a GCA_022448505.1_ASM2244850v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:46:44,136] [INFO] Task succeeded: Prodigal
[2023-06-13 16:46:44,137] [INFO] Task started: HMMsearch
[2023-06-13 16:46:44,137] [INFO] Running command: hmmsearch --tblout GCA_022448505.1_ASM2244850v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference/reference_markers.hmm GCA_022448505.1_ASM2244850v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:46:44,326] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:46:44,327] [INFO] Found 6/6 markers.
[2023-06-13 16:46:44,357] [INFO] Query marker FASTA was written to GCA_022448505.1_ASM2244850v1_genomic.fna/markers.fasta
[2023-06-13 16:46:44,358] [INFO] Task started: Blastn
[2023-06-13 16:46:44,358] [INFO] Running command: blastn -query GCA_022448505.1_ASM2244850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference/reference_markers.fasta -out GCA_022448505.1_ASM2244850v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:46:44,928] [INFO] Task succeeded: Blastn
[2023-06-13 16:46:44,931] [INFO] Selected 16 target genomes.
[2023-06-13 16:46:44,932] [INFO] Target genome list was writen to GCA_022448505.1_ASM2244850v1_genomic.fna/target_genomes.txt
[2023-06-13 16:46:44,935] [INFO] Task started: fastANI
[2023-06-13 16:46:44,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb9ec11-3335-42ab-bca3-2e0100b458ba/GCA_022448505.1_ASM2244850v1_genomic.fna.gz --refList GCA_022448505.1_ASM2244850v1_genomic.fna/target_genomes.txt --output GCA_022448505.1_ASM2244850v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:46:53,938] [INFO] Task succeeded: fastANI
[2023-06-13 16:46:53,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:46:53,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:46:53,940] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:46:53,940] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 16:46:53,940] [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
--------------------------------------------------------------------------------
[2023-06-13 16:46:53,942] [INFO] DFAST Taxonomy check result was written to GCA_022448505.1_ASM2244850v1_genomic.fna/tc_result.tsv
[2023-06-13 16:46:53,942] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:46:53,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:46:53,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference/checkm_data
[2023-06-13 16:46:53,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:46:53,980] [INFO] Task started: CheckM
[2023-06-13 16:46:53,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448505.1_ASM2244850v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448505.1_ASM2244850v1_genomic.fna/checkm_input GCA_022448505.1_ASM2244850v1_genomic.fna/checkm_result
[2023-06-13 16:47:26,394] [INFO] Task succeeded: CheckM
[2023-06-13 16:47:26,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:47:26,413] [INFO] ===== Completeness check finished =====
[2023-06-13 16:47:26,413] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:47:26,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448505.1_ASM2244850v1_genomic.fna/markers.fasta)
[2023-06-13 16:47:26,413] [INFO] Task started: Blastn
[2023-06-13 16:47:26,413] [INFO] Running command: blastn -query GCA_022448505.1_ASM2244850v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b667c13-2605-4e1d-829b-a3e09ecfb75e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448505.1_ASM2244850v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:47:27,204] [INFO] Task succeeded: Blastn
[2023-06-13 16:47:27,207] [INFO] Selected 14 target genomes.
[2023-06-13 16:47:27,208] [INFO] Target genome list was writen to GCA_022448505.1_ASM2244850v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:47:27,222] [INFO] Task started: fastANI
[2023-06-13 16:47:27,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg2bb9ec11-3335-42ab-bca3-2e0100b458ba/GCA_022448505.1_ASM2244850v1_genomic.fna.gz --refList GCA_022448505.1_ASM2244850v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448505.1_ASM2244850v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:47:35,915] [INFO] Task succeeded: fastANI
[2023-06-13 16:47:35,920] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:47:35,921] [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_002313895.1	s__UBA1123 sp002313895	97.7713	964	1155	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA11138;g__UBA1123	95.0	98.51	97.41	0.87	0.77	6	conclusive
GCA_002710885.1	s__UBA1123 sp002710885	94.7993	683	1155	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA11138;g__UBA1123	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328865.1	s__UBA2160 sp002328865	76.132	98	1155	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA11138;g__UBA2160	95.0	99.82	99.77	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2023-06-13 16:47:35,923] [INFO] GTDB search result was written to GCA_022448505.1_ASM2244850v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:47:35,924] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:47:35,927] [INFO] DFAST_QC result json was written to GCA_022448505.1_ASM2244850v1_genomic.fna/dqc_result.json
[2023-06-13 16:47:35,927] [INFO] DFAST_QC completed!
[2023-06-13 16:47:35,927] [INFO] Total running time: 0h1m3s