[2023-06-29 12:40:57,394] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:40:57,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:40:57,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference
[2023-06-29 12:40:58,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:40:58,614] [INFO] Task started: Prodigal
[2023-06-29 12:40:58,615] [INFO] Running command: gunzip -c /var/lib/cwl/stg48887243-32df-4b4e-b6b1-5a59c3581313/GCA_021741955.1_ASM2174195v1_genomic.fna.gz | prodigal -d GCA_021741955.1_ASM2174195v1_genomic.fna/cds.fna -a GCA_021741955.1_ASM2174195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:41:01,372] [INFO] Task succeeded: Prodigal
[2023-06-29 12:41:01,372] [INFO] Task started: HMMsearch
[2023-06-29 12:41:01,373] [INFO] Running command: hmmsearch --tblout GCA_021741955.1_ASM2174195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference/reference_markers.hmm GCA_021741955.1_ASM2174195v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:41:01,556] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:41:01,557] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg48887243-32df-4b4e-b6b1-5a59c3581313/GCA_021741955.1_ASM2174195v1_genomic.fna.gz]
[2023-06-29 12:41:01,576] [INFO] Query marker FASTA was written to GCA_021741955.1_ASM2174195v1_genomic.fna/markers.fasta
[2023-06-29 12:41:01,576] [INFO] Task started: Blastn
[2023-06-29 12:41:01,576] [INFO] Running command: blastn -query GCA_021741955.1_ASM2174195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference/reference_markers.fasta -out GCA_021741955.1_ASM2174195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:02,061] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:02,065] [INFO] Selected 10 target genomes.
[2023-06-29 12:41:02,066] [INFO] Target genome list was writen to GCA_021741955.1_ASM2174195v1_genomic.fna/target_genomes.txt
[2023-06-29 12:41:02,070] [INFO] Task started: fastANI
[2023-06-29 12:41:02,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg48887243-32df-4b4e-b6b1-5a59c3581313/GCA_021741955.1_ASM2174195v1_genomic.fna.gz --refList GCA_021741955.1_ASM2174195v1_genomic.fna/target_genomes.txt --output GCA_021741955.1_ASM2174195v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:41:06,588] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:06,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:41:06,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:41:06,591] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:41:06,591] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:41:06,591] [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 12:41:06,594] [INFO] DFAST Taxonomy check result was written to GCA_021741955.1_ASM2174195v1_genomic.fna/tc_result.tsv
[2023-06-29 12:41:06,595] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:41:06,595] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:41:06,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference/checkm_data
[2023-06-29 12:41:06,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:41:06,615] [INFO] Task started: CheckM
[2023-06-29 12:41:06,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021741955.1_ASM2174195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021741955.1_ASM2174195v1_genomic.fna/checkm_input GCA_021741955.1_ASM2174195v1_genomic.fna/checkm_result
[2023-06-29 12:41:22,428] [INFO] Task succeeded: CheckM
[2023-06-29 12:41:22,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:41:22,449] [INFO] ===== Completeness check finished =====
[2023-06-29 12:41:22,450] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:41:22,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021741955.1_ASM2174195v1_genomic.fna/markers.fasta)
[2023-06-29 12:41:22,451] [INFO] Task started: Blastn
[2023-06-29 12:41:22,451] [INFO] Running command: blastn -query GCA_021741955.1_ASM2174195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg586caff6-6867-4c3b-968b-864edb331329/dqc_reference/reference_markers_gtdb.fasta -out GCA_021741955.1_ASM2174195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:22,902] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:22,907] [INFO] Selected 9 target genomes.
[2023-06-29 12:41:22,907] [INFO] Target genome list was writen to GCA_021741955.1_ASM2174195v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:41:22,924] [INFO] Task started: fastANI
[2023-06-29 12:41:22,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg48887243-32df-4b4e-b6b1-5a59c3581313/GCA_021741955.1_ASM2174195v1_genomic.fna.gz --refList GCA_021741955.1_ASM2174195v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021741955.1_ASM2174195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:41:25,458] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:25,463] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:41:25,463] [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_002430405.1	s__UBA5976 sp002430405	93.9102	231	364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702945.1	s__UBA5976 sp009702945	79.5253	81	364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009698575.1	s__UBA5976 sp009698575	78.7288	145	364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.89	99.66	0.97	0.94	7	-
GCA_903925705.1	s__UBA5976 sp903925705	78.6321	96	364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:41:25,465] [INFO] GTDB search result was written to GCA_021741955.1_ASM2174195v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:41:25,466] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:41:25,469] [INFO] DFAST_QC result json was written to GCA_021741955.1_ASM2174195v1_genomic.fna/dqc_result.json
[2023-06-29 12:41:25,469] [INFO] DFAST_QC completed!
[2023-06-29 12:41:25,469] [INFO] Total running time: 0h0m28s