[2023-06-05 05:15:46,959] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:46,967] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:46,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference
[2023-06-05 05:15:48,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:48,156] [INFO] Task started: Prodigal
[2023-06-05 05:15:48,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg72863112-b4f1-4723-a21b-5d9fe2544379/GCA_001797355.1_ASM179735v1_genomic.fna.gz | prodigal -d GCA_001797355.1_ASM179735v1_genomic.fna/cds.fna -a GCA_001797355.1_ASM179735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:52,618] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:52,619] [INFO] Task started: HMMsearch
[2023-06-05 05:15:52,619] [INFO] Running command: hmmsearch --tblout GCA_001797355.1_ASM179735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference/reference_markers.hmm GCA_001797355.1_ASM179735v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:52,860] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:52,862] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg72863112-b4f1-4723-a21b-5d9fe2544379/GCA_001797355.1_ASM179735v1_genomic.fna.gz]
[2023-06-05 05:15:52,898] [INFO] Query marker FASTA was written to GCA_001797355.1_ASM179735v1_genomic.fna/markers.fasta
[2023-06-05 05:15:52,899] [INFO] Task started: Blastn
[2023-06-05 05:15:52,899] [INFO] Running command: blastn -query GCA_001797355.1_ASM179735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference/reference_markers.fasta -out GCA_001797355.1_ASM179735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:15:53,449] [INFO] Task succeeded: Blastn
[2023-06-05 05:15:53,453] [INFO] Selected 10 target genomes.
[2023-06-05 05:15:53,454] [INFO] Target genome list was writen to GCA_001797355.1_ASM179735v1_genomic.fna/target_genomes.txt
[2023-06-05 05:15:53,455] [INFO] Task started: fastANI
[2023-06-05 05:15:53,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg72863112-b4f1-4723-a21b-5d9fe2544379/GCA_001797355.1_ASM179735v1_genomic.fna.gz --refList GCA_001797355.1_ASM179735v1_genomic.fna/target_genomes.txt --output GCA_001797355.1_ASM179735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:15:58,781] [INFO] Task succeeded: fastANI
[2023-06-05 05:15:58,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:15:58,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:15:58,784] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:15:58,785] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:15:58,785] [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
--------------------------------------------------------------------------------
[2023-06-05 05:15:58,787] [INFO] DFAST Taxonomy check result was written to GCA_001797355.1_ASM179735v1_genomic.fna/tc_result.tsv
[2023-06-05 05:15:58,787] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:15:58,787] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:15:58,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference/checkm_data
[2023-06-05 05:15:58,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:15:58,816] [INFO] Task started: CheckM
[2023-06-05 05:15:58,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001797355.1_ASM179735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001797355.1_ASM179735v1_genomic.fna/checkm_input GCA_001797355.1_ASM179735v1_genomic.fna/checkm_result
[2023-06-05 05:16:19,513] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:19,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:19,535] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:19,535] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:19,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001797355.1_ASM179735v1_genomic.fna/markers.fasta)
[2023-06-05 05:16:19,536] [INFO] Task started: Blastn
[2023-06-05 05:16:19,536] [INFO] Running command: blastn -query GCA_001797355.1_ASM179735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4421f02a-d74a-4058-bcb7-35def6d1ca0d/dqc_reference/reference_markers_gtdb.fasta -out GCA_001797355.1_ASM179735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:20,257] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:20,262] [INFO] Selected 12 target genomes.
[2023-06-05 05:16:20,262] [INFO] Target genome list was writen to GCA_001797355.1_ASM179735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:20,271] [INFO] Task started: fastANI
[2023-06-05 05:16:20,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg72863112-b4f1-4723-a21b-5d9fe2544379/GCA_001797355.1_ASM179735v1_genomic.fna.gz --refList GCA_001797355.1_ASM179735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001797355.1_ASM179735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:16:26,433] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:26,441] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:16:26,441] [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_001798165.1	s__UBA10170 sp001798165	99.8506	578	673	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__UBA9637;f__UBA9637;g__UBA10170	95.0	99.89	99.80	0.88	0.86	4	conclusive
GCA_016195725.1	s__UBA10170 sp016195725	81.1579	357	673	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__UBA9637;f__UBA9637;g__UBA10170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234985.1	s__JACRNJ01 sp016234985	80.0413	165	673	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__UBA9637;f__UBA9637;g__JACRNJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219285.1	s__JACRNJ01 sp016219285	79.2838	265	673	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__UBA9637;f__UBA9637;g__JACRNJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200645.1	s__JACRNJ01 sp016200645	78.993	238	673	d__Bacteria;p__Desulfobacterota;c__GWC2-55-46;o__UBA9637;f__UBA9637;g__JACRNJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:16:26,443] [INFO] GTDB search result was written to GCA_001797355.1_ASM179735v1_genomic.fna/result_gtdb.tsv
[2023-06-05 05:16:26,443] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:16:26,446] [INFO] DFAST_QC result json was written to GCA_001797355.1_ASM179735v1_genomic.fna/dqc_result.json
[2023-06-05 05:16:26,446] [INFO] DFAST_QC completed!
[2023-06-05 05:16:26,446] [INFO] Total running time: 0h0m39s