[2023-06-27 08:15:51,983] [INFO] DFAST_QC pipeline started.
[2023-06-27 08:15:51,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 08:15:51,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference
[2023-06-27 08:15:53,253] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 08:15:53,254] [INFO] Task started: Prodigal
[2023-06-27 08:15:53,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ae2ec4a-f3a7-4fd1-93d6-a2f739a9f372/GCA_002433405.1_ASM243340v1_genomic.fna.gz | prodigal -d GCA_002433405.1_ASM243340v1_genomic.fna/cds.fna -a GCA_002433405.1_ASM243340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 08:16:00,515] [INFO] Task succeeded: Prodigal
[2023-06-27 08:16:00,516] [INFO] Task started: HMMsearch
[2023-06-27 08:16:00,516] [INFO] Running command: hmmsearch --tblout GCA_002433405.1_ASM243340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference/reference_markers.hmm GCA_002433405.1_ASM243340v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 08:16:00,757] [INFO] Task succeeded: HMMsearch
[2023-06-27 08:16:00,758] [INFO] Found 6/6 markers.
[2023-06-27 08:16:00,794] [INFO] Query marker FASTA was written to GCA_002433405.1_ASM243340v1_genomic.fna/markers.fasta
[2023-06-27 08:16:00,794] [INFO] Task started: Blastn
[2023-06-27 08:16:00,795] [INFO] Running command: blastn -query GCA_002433405.1_ASM243340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference/reference_markers.fasta -out GCA_002433405.1_ASM243340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:16:01,466] [INFO] Task succeeded: Blastn
[2023-06-27 08:16:01,470] [INFO] Selected 25 target genomes.
[2023-06-27 08:16:01,470] [INFO] Target genome list was writen to GCA_002433405.1_ASM243340v1_genomic.fna/target_genomes.txt
[2023-06-27 08:16:01,478] [INFO] Task started: fastANI
[2023-06-27 08:16:01,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ae2ec4a-f3a7-4fd1-93d6-a2f739a9f372/GCA_002433405.1_ASM243340v1_genomic.fna.gz --refList GCA_002433405.1_ASM243340v1_genomic.fna/target_genomes.txt --output GCA_002433405.1_ASM243340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 08:16:15,955] [INFO] Task succeeded: fastANI
[2023-06-27 08:16:15,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 08:16:15,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 08:16:15,957] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 08:16:15,957] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 08:16:15,957] [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 08:16:15,960] [INFO] DFAST Taxonomy check result was written to GCA_002433405.1_ASM243340v1_genomic.fna/tc_result.tsv
[2023-06-27 08:16:15,960] [INFO] ===== Taxonomy check completed =====
[2023-06-27 08:16:15,961] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 08:16:15,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference/checkm_data
[2023-06-27 08:16:15,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 08:16:16,005] [INFO] Task started: CheckM
[2023-06-27 08:16:16,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002433405.1_ASM243340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002433405.1_ASM243340v1_genomic.fna/checkm_input GCA_002433405.1_ASM243340v1_genomic.fna/checkm_result
[2023-06-27 08:16:43,629] [INFO] Task succeeded: CheckM
[2023-06-27 08:16:43,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 08:16:43,682] [INFO] ===== Completeness check finished =====
[2023-06-27 08:16:43,682] [INFO] ===== Start GTDB Search =====
[2023-06-27 08:16:43,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002433405.1_ASM243340v1_genomic.fna/markers.fasta)
[2023-06-27 08:16:43,683] [INFO] Task started: Blastn
[2023-06-27 08:16:43,683] [INFO] Running command: blastn -query GCA_002433405.1_ASM243340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc447702b-5821-4701-83b9-ad8795b6ded3/dqc_reference/reference_markers_gtdb.fasta -out GCA_002433405.1_ASM243340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:16:44,673] [INFO] Task succeeded: Blastn
[2023-06-27 08:16:44,677] [INFO] Selected 24 target genomes.
[2023-06-27 08:16:44,678] [INFO] Target genome list was writen to GCA_002433405.1_ASM243340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 08:16:44,709] [INFO] Task started: fastANI
[2023-06-27 08:16:44,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ae2ec4a-f3a7-4fd1-93d6-a2f739a9f372/GCA_002433405.1_ASM243340v1_genomic.fna.gz --refList GCA_002433405.1_ASM243340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002433405.1_ASM243340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 08:16:56,063] [INFO] Task succeeded: fastANI
[2023-06-27 08:16:56,072] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-27 08:16:56,072] [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_002937455.1	s__UBA830 sp002937455	99.8997	799	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	99.94	99.90	0.94	0.84	5	inconclusive
GCA_002718135.1	s__AG-337-I02 sp002718135	99.2409	78	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002471575.1	s__UBA830 sp002471575	76.5081	117	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	97.90	95.90	0.91	0.84	7	-
GCA_905479125.1	s__UBA830 sp905479125	75.6022	58	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
GCA_905181725.1	s__UBA830 sp905181725	75.4951	52	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 08:16:56,074] [INFO] GTDB search result was written to GCA_002433405.1_ASM243340v1_genomic.fna/result_gtdb.tsv
[2023-06-27 08:16:56,075] [INFO] ===== GTDB Search completed =====
[2023-06-27 08:16:56,088] [INFO] DFAST_QC result json was written to GCA_002433405.1_ASM243340v1_genomic.fna/dqc_result.json
[2023-06-27 08:16:56,088] [INFO] DFAST_QC completed!
[2023-06-27 08:16:56,088] [INFO] Total running time: 0h1m4s