[2023-06-16 19:03:14,358] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:03:14,361] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:03:14,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference
[2023-06-16 19:03:15,615] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:03:15,616] [INFO] Task started: Prodigal
[2023-06-16 19:03:15,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg663a9b0b-1294-4aa7-bb72-a52b2091a979/GCA_003672465.1_ASM367246v1_genomic.fna.gz | prodigal -d GCA_003672465.1_ASM367246v1_genomic.fna/cds.fna -a GCA_003672465.1_ASM367246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:03:18,153] [INFO] Task succeeded: Prodigal
[2023-06-16 19:03:18,153] [INFO] Task started: HMMsearch
[2023-06-16 19:03:18,153] [INFO] Running command: hmmsearch --tblout GCA_003672465.1_ASM367246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference/reference_markers.hmm GCA_003672465.1_ASM367246v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:03:18,372] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:03:18,374] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg663a9b0b-1294-4aa7-bb72-a52b2091a979/GCA_003672465.1_ASM367246v1_genomic.fna.gz]
[2023-06-16 19:03:18,402] [INFO] Query marker FASTA was written to GCA_003672465.1_ASM367246v1_genomic.fna/markers.fasta
[2023-06-16 19:03:18,402] [INFO] Task started: Blastn
[2023-06-16 19:03:18,402] [INFO] Running command: blastn -query GCA_003672465.1_ASM367246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference/reference_markers.fasta -out GCA_003672465.1_ASM367246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:03:18,913] [INFO] Task succeeded: Blastn
[2023-06-16 19:03:18,917] [INFO] Selected 2 target genomes.
[2023-06-16 19:03:18,918] [INFO] Target genome list was writen to GCA_003672465.1_ASM367246v1_genomic.fna/target_genomes.txt
[2023-06-16 19:03:18,920] [INFO] Task started: fastANI
[2023-06-16 19:03:18,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg663a9b0b-1294-4aa7-bb72-a52b2091a979/GCA_003672465.1_ASM367246v1_genomic.fna.gz --refList GCA_003672465.1_ASM367246v1_genomic.fna/target_genomes.txt --output GCA_003672465.1_ASM367246v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:03:20,330] [INFO] Task succeeded: fastANI
[2023-06-16 19:03:20,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:03:20,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:03:20,333] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:03:20,334] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:03:20,334] [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
--------------------------------------------------------------------------------
[2023-06-16 19:03:20,337] [INFO] DFAST Taxonomy check result was written to GCA_003672465.1_ASM367246v1_genomic.fna/tc_result.tsv
[2023-06-16 19:03:20,338] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:03:20,338] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:03:20,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference/checkm_data
[2023-06-16 19:03:20,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:03:20,359] [INFO] Task started: CheckM
[2023-06-16 19:03:20,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003672465.1_ASM367246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003672465.1_ASM367246v1_genomic.fna/checkm_input GCA_003672465.1_ASM367246v1_genomic.fna/checkm_result
[2023-06-16 19:03:36,556] [INFO] Task succeeded: CheckM
[2023-06-16 19:03:36,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.70%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:03:36,581] [INFO] ===== Completeness check finished =====
[2023-06-16 19:03:36,581] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:03:36,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003672465.1_ASM367246v1_genomic.fna/markers.fasta)
[2023-06-16 19:03:36,582] [INFO] Task started: Blastn
[2023-06-16 19:03:36,582] [INFO] Running command: blastn -query GCA_003672465.1_ASM367246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44e086db-258b-4348-8081-c2b6e735c21b/dqc_reference/reference_markers_gtdb.fasta -out GCA_003672465.1_ASM367246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:03:37,954] [INFO] Task succeeded: Blastn
[2023-06-16 19:03:37,958] [INFO] Selected 11 target genomes.
[2023-06-16 19:03:37,958] [INFO] Target genome list was writen to GCA_003672465.1_ASM367246v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:03:37,984] [INFO] Task started: fastANI
[2023-06-16 19:03:37,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg663a9b0b-1294-4aa7-bb72-a52b2091a979/GCA_003672465.1_ASM367246v1_genomic.fna.gz --refList GCA_003672465.1_ASM367246v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003672465.1_ASM367246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:03:41,336] [INFO] Task succeeded: fastANI
[2023-06-16 19:03:41,347] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:03:41,348] [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_002714745.1	s__Thalassarchaeum sp002714745	98.9038	249	312	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	97.82	95.69	0.77	0.69	7	conclusive
GCA_002727275.1	s__Thalassarchaeum sp002727275	81.5492	223	312	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698225.1	s__Thalassarchaeum sp002698225	81.0924	193	312	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	-
GCA_002501885.1	s__Thalassarchaeum sp002501885	79.4121	181	312	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	-
GCA_002495735.1	s__Thalassarchaeum sp002495735	77.1231	76	312	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:03:41,359] [INFO] GTDB search result was written to GCA_003672465.1_ASM367246v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:03:41,360] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:03:41,363] [INFO] DFAST_QC result json was written to GCA_003672465.1_ASM367246v1_genomic.fna/dqc_result.json
[2023-06-16 19:03:41,363] [INFO] DFAST_QC completed!
[2023-06-16 19:03:41,363] [INFO] Total running time: 0h0m27s