[2023-06-29 15:40:12,913] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:40:12,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:40:12,915] [INFO] DQC Reference Directory: /var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference
[2023-06-29 15:40:15,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:40:15,136] [INFO] Task started: Prodigal
[2023-06-29 15:40:15,136] [INFO] Running command: gunzip -c /var/lib/cwl/stg68bfae2c-93dc-4c77-a7cd-f749760f53af/GCA_021372055.1_ASM2137205v1_genomic.fna.gz | prodigal -d GCA_021372055.1_ASM2137205v1_genomic.fna/cds.fna -a GCA_021372055.1_ASM2137205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:40:26,844] [INFO] Task succeeded: Prodigal
[2023-06-29 15:40:26,845] [INFO] Task started: HMMsearch
[2023-06-29 15:40:26,845] [INFO] Running command: hmmsearch --tblout GCA_021372055.1_ASM2137205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference/reference_markers.hmm GCA_021372055.1_ASM2137205v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:40:27,129] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:40:27,131] [INFO] Found 6/6 markers.
[2023-06-29 15:40:27,173] [INFO] Query marker FASTA was written to GCA_021372055.1_ASM2137205v1_genomic.fna/markers.fasta
[2023-06-29 15:40:27,174] [INFO] Task started: Blastn
[2023-06-29 15:40:27,174] [INFO] Running command: blastn -query GCA_021372055.1_ASM2137205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference/reference_markers.fasta -out GCA_021372055.1_ASM2137205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:40:27,765] [INFO] Task succeeded: Blastn
[2023-06-29 15:40:27,770] [INFO] Selected 25 target genomes.
[2023-06-29 15:40:27,770] [INFO] Target genome list was writen to GCA_021372055.1_ASM2137205v1_genomic.fna/target_genomes.txt
[2023-06-29 15:40:27,771] [INFO] Task started: fastANI
[2023-06-29 15:40:27,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg68bfae2c-93dc-4c77-a7cd-f749760f53af/GCA_021372055.1_ASM2137205v1_genomic.fna.gz --refList GCA_021372055.1_ASM2137205v1_genomic.fna/target_genomes.txt --output GCA_021372055.1_ASM2137205v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:40:41,292] [INFO] Task succeeded: fastANI
[2023-06-29 15:40:41,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:40:41,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:40:41,299] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:40:41,299] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:40:41,299] [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
Syntrophobacter fumaroxidans	strain=MPOB	GCA_000014965.1	119484	119484	type	True	76.2419	123	1398	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:40:41,301] [INFO] DFAST Taxonomy check result was written to GCA_021372055.1_ASM2137205v1_genomic.fna/tc_result.tsv
[2023-06-29 15:40:41,302] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:40:41,302] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:40:41,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference/checkm_data
[2023-06-29 15:40:41,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:40:41,350] [INFO] Task started: CheckM
[2023-06-29 15:40:41,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021372055.1_ASM2137205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021372055.1_ASM2137205v1_genomic.fna/checkm_input GCA_021372055.1_ASM2137205v1_genomic.fna/checkm_result
[2023-06-29 15:41:19,212] [INFO] Task succeeded: CheckM
[2023-06-29 15:41:19,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 10.65%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:41:19,239] [INFO] ===== Completeness check finished =====
[2023-06-29 15:41:19,239] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:41:19,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021372055.1_ASM2137205v1_genomic.fna/markers.fasta)
[2023-06-29 15:41:19,240] [INFO] Task started: Blastn
[2023-06-29 15:41:19,240] [INFO] Running command: blastn -query GCA_021372055.1_ASM2137205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62fc3ddb-f0fc-4f9c-b101-c4a7c6441fc2/dqc_reference/reference_markers_gtdb.fasta -out GCA_021372055.1_ASM2137205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:41:20,046] [INFO] Task succeeded: Blastn
[2023-06-29 15:41:20,051] [INFO] Selected 23 target genomes.
[2023-06-29 15:41:20,051] [INFO] Target genome list was writen to GCA_021372055.1_ASM2137205v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:41:20,076] [INFO] Task started: fastANI
[2023-06-29 15:41:20,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg68bfae2c-93dc-4c77-a7cd-f749760f53af/GCA_021372055.1_ASM2137205v1_genomic.fna.gz --refList GCA_021372055.1_ASM2137205v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021372055.1_ASM2137205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:41:33,117] [INFO] Task succeeded: fastANI
[2023-06-29 15:41:33,130] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:41:33,131] [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_001603845.1	s__SbD1 sp001603845	77.2731	146	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165235.1	s__SbD1 sp003165235	76.8061	147	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298995.1	s__SbD1 sp002298995	76.7531	127	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290365.1	s__SbD1 sp900290365	76.6921	103	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298165.1	s__SbD1 sp002298165	76.3979	109	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014965.1	s__Syntrophobacter fumaroxidans	76.2706	121	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__Syntrophobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013314815.1	s__JABUEY01 sp013314815	76.2627	84	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JABUEY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517315.1	s__JAAYUJ01 sp012517315	76.1358	67	1398	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAAYUJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:41:33,133] [INFO] GTDB search result was written to GCA_021372055.1_ASM2137205v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:41:33,133] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:41:33,136] [INFO] DFAST_QC result json was written to GCA_021372055.1_ASM2137205v1_genomic.fna/dqc_result.json
[2023-06-29 15:41:33,137] [INFO] DFAST_QC completed!
[2023-06-29 15:41:33,137] [INFO] Total running time: 0h1m20s