[2023-06-17 05:26:50,500] [INFO] DFAST_QC pipeline started.
[2023-06-17 05:26:50,504] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 05:26:50,504] [INFO] DQC Reference Directory: /var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference
[2023-06-17 05:26:52,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 05:26:52,543] [INFO] Task started: Prodigal
[2023-06-17 05:26:52,543] [INFO] Running command: gunzip -c /var/lib/cwl/stg036d6513-c5aa-4094-91ee-d1b0c2b1ecff/GCA_028707255.1_ASM2870725v1_genomic.fna.gz | prodigal -d GCA_028707255.1_ASM2870725v1_genomic.fna/cds.fna -a GCA_028707255.1_ASM2870725v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 05:26:56,085] [INFO] Task succeeded: Prodigal
[2023-06-17 05:26:56,086] [INFO] Task started: HMMsearch
[2023-06-17 05:26:56,086] [INFO] Running command: hmmsearch --tblout GCA_028707255.1_ASM2870725v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference/reference_markers.hmm GCA_028707255.1_ASM2870725v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 05:26:56,303] [INFO] Task succeeded: HMMsearch
[2023-06-17 05:26:56,304] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg036d6513-c5aa-4094-91ee-d1b0c2b1ecff/GCA_028707255.1_ASM2870725v1_genomic.fna.gz]
[2023-06-17 05:26:56,328] [INFO] Query marker FASTA was written to GCA_028707255.1_ASM2870725v1_genomic.fna/markers.fasta
[2023-06-17 05:26:56,329] [INFO] Task started: Blastn
[2023-06-17 05:26:56,329] [INFO] Running command: blastn -query GCA_028707255.1_ASM2870725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference/reference_markers.fasta -out GCA_028707255.1_ASM2870725v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:26:56,895] [INFO] Task succeeded: Blastn
[2023-06-17 05:26:56,900] [INFO] Selected 18 target genomes.
[2023-06-17 05:26:56,900] [INFO] Target genome list was writen to GCA_028707255.1_ASM2870725v1_genomic.fna/target_genomes.txt
[2023-06-17 05:26:56,906] [INFO] Task started: fastANI
[2023-06-17 05:26:56,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg036d6513-c5aa-4094-91ee-d1b0c2b1ecff/GCA_028707255.1_ASM2870725v1_genomic.fna.gz --refList GCA_028707255.1_ASM2870725v1_genomic.fna/target_genomes.txt --output GCA_028707255.1_ASM2870725v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 05:27:07,960] [INFO] Task succeeded: fastANI
[2023-06-17 05:27:07,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 05:27:07,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 05:27:07,962] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 05:27:07,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 05:27:07,963] [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
--------------------------------------------------------------------------------
[2023-06-17 05:27:07,965] [INFO] DFAST Taxonomy check result was written to GCA_028707255.1_ASM2870725v1_genomic.fna/tc_result.tsv
[2023-06-17 05:27:07,966] [INFO] ===== Taxonomy check completed =====
[2023-06-17 05:27:07,967] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 05:27:07,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference/checkm_data
[2023-06-17 05:27:07,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 05:27:07,994] [INFO] Task started: CheckM
[2023-06-17 05:27:07,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028707255.1_ASM2870725v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028707255.1_ASM2870725v1_genomic.fna/checkm_input GCA_028707255.1_ASM2870725v1_genomic.fna/checkm_result
[2023-06-17 05:27:25,979] [INFO] Task succeeded: CheckM
[2023-06-17 05:27:25,981] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 05:27:26,008] [INFO] ===== Completeness check finished =====
[2023-06-17 05:27:26,008] [INFO] ===== Start GTDB Search =====
[2023-06-17 05:27:26,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028707255.1_ASM2870725v1_genomic.fna/markers.fasta)
[2023-06-17 05:27:26,009] [INFO] Task started: Blastn
[2023-06-17 05:27:26,009] [INFO] Running command: blastn -query GCA_028707255.1_ASM2870725v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee4b15e9-9811-4ab2-9812-5efb736255cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_028707255.1_ASM2870725v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 05:27:26,786] [INFO] Task succeeded: Blastn
[2023-06-17 05:27:26,791] [INFO] Selected 11 target genomes.
[2023-06-17 05:27:26,791] [INFO] Target genome list was writen to GCA_028707255.1_ASM2870725v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 05:27:26,804] [INFO] Task started: fastANI
[2023-06-17 05:27:26,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg036d6513-c5aa-4094-91ee-d1b0c2b1ecff/GCA_028707255.1_ASM2870725v1_genomic.fna.gz --refList GCA_028707255.1_ASM2870725v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028707255.1_ASM2870725v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 05:27:30,111] [INFO] Task succeeded: fastANI
[2023-06-17 05:27:30,122] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 05:27:30,122] [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_002421585.1	s__UBA5627 sp002421585	82.1018	249	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419135.1	s__UBA5627 sp002419135	81.6313	295	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719115.1	s__UBA5627 sp012719115	81.3843	216	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520835.1	s__UBA5627 sp012520835	81.0617	212	512	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__Dehalococcoidales;f__UBA5627;g__UBA5627	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 05:27:30,125] [INFO] GTDB search result was written to GCA_028707255.1_ASM2870725v1_genomic.fna/result_gtdb.tsv
[2023-06-17 05:27:30,125] [INFO] ===== GTDB Search completed =====
[2023-06-17 05:27:30,128] [INFO] DFAST_QC result json was written to GCA_028707255.1_ASM2870725v1_genomic.fna/dqc_result.json
[2023-06-17 05:27:30,128] [INFO] DFAST_QC completed!
[2023-06-17 05:27:30,128] [INFO] Total running time: 0h0m40s