[2023-06-27 17:17:34,605] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:17:34,608] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:17:34,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference
[2023-06-27 17:17:36,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:17:36,050] [INFO] Task started: Prodigal
[2023-06-27 17:17:36,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e76c03-7405-4001-bc1a-1dff9fdae7f6/GCA_002494485.1_ASM249448v1_genomic.fna.gz | prodigal -d GCA_002494485.1_ASM249448v1_genomic.fna/cds.fna -a GCA_002494485.1_ASM249448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:17:38,320] [INFO] Task succeeded: Prodigal
[2023-06-27 17:17:38,321] [INFO] Task started: HMMsearch
[2023-06-27 17:17:38,321] [INFO] Running command: hmmsearch --tblout GCA_002494485.1_ASM249448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference/reference_markers.hmm GCA_002494485.1_ASM249448v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:17:38,504] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:17:38,505] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg40e76c03-7405-4001-bc1a-1dff9fdae7f6/GCA_002494485.1_ASM249448v1_genomic.fna.gz]
[2023-06-27 17:17:38,528] [INFO] Query marker FASTA was written to GCA_002494485.1_ASM249448v1_genomic.fna/markers.fasta
[2023-06-27 17:17:38,529] [INFO] Task started: Blastn
[2023-06-27 17:17:38,529] [INFO] Running command: blastn -query GCA_002494485.1_ASM249448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference/reference_markers.fasta -out GCA_002494485.1_ASM249448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:17:39,059] [INFO] Task succeeded: Blastn
[2023-06-27 17:17:39,063] [INFO] Selected 5 target genomes.
[2023-06-27 17:17:39,064] [INFO] Target genome list was writen to GCA_002494485.1_ASM249448v1_genomic.fna/target_genomes.txt
[2023-06-27 17:17:39,066] [INFO] Task started: fastANI
[2023-06-27 17:17:39,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e76c03-7405-4001-bc1a-1dff9fdae7f6/GCA_002494485.1_ASM249448v1_genomic.fna.gz --refList GCA_002494485.1_ASM249448v1_genomic.fna/target_genomes.txt --output GCA_002494485.1_ASM249448v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:17:42,440] [INFO] Task succeeded: fastANI
[2023-06-27 17:17:42,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:17:42,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:17:42,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:17:42,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 17:17:42,443] [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
--------------------------------------------------------------------------------
[2023-06-27 17:17:42,446] [INFO] DFAST Taxonomy check result was written to GCA_002494485.1_ASM249448v1_genomic.fna/tc_result.tsv
[2023-06-27 17:17:42,446] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:17:42,446] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:17:42,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference/checkm_data
[2023-06-27 17:17:42,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:17:42,475] [INFO] Task started: CheckM
[2023-06-27 17:17:42,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002494485.1_ASM249448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002494485.1_ASM249448v1_genomic.fna/checkm_input GCA_002494485.1_ASM249448v1_genomic.fna/checkm_result
[2023-06-27 17:17:57,682] [INFO] Task succeeded: CheckM
[2023-06-27 17:17:57,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.92%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 17:17:57,706] [INFO] ===== Completeness check finished =====
[2023-06-27 17:17:57,707] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:17:57,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002494485.1_ASM249448v1_genomic.fna/markers.fasta)
[2023-06-27 17:17:57,708] [INFO] Task started: Blastn
[2023-06-27 17:17:57,708] [INFO] Running command: blastn -query GCA_002494485.1_ASM249448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ae27aa-5975-42d4-a090-f30a210bd6ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_002494485.1_ASM249448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:17:58,402] [INFO] Task succeeded: Blastn
[2023-06-27 17:17:58,407] [INFO] Selected 7 target genomes.
[2023-06-27 17:17:58,407] [INFO] Target genome list was writen to GCA_002494485.1_ASM249448v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:17:58,412] [INFO] Task started: fastANI
[2023-06-27 17:17:58,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e76c03-7405-4001-bc1a-1dff9fdae7f6/GCA_002494485.1_ASM249448v1_genomic.fna.gz --refList GCA_002494485.1_ASM249448v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002494485.1_ASM249448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:17:59,969] [INFO] Task succeeded: fastANI
[2023-06-27 17:17:59,973] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:17:59,973] [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_002713325.1	s__UBA213 sp002713325	99.5412	275	341	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA213;g__UBA213	95.0	98.35	97.23	0.79	0.76	3	conclusive
--------------------------------------------------------------------------------
[2023-06-27 17:17:59,975] [INFO] GTDB search result was written to GCA_002494485.1_ASM249448v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:17:59,976] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:17:59,979] [INFO] DFAST_QC result json was written to GCA_002494485.1_ASM249448v1_genomic.fna/dqc_result.json
[2023-06-27 17:17:59,979] [INFO] DFAST_QC completed!
[2023-06-27 17:17:59,980] [INFO] Total running time: 0h0m25s