[2023-06-18 19:17:04,951] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:17:04,960] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:17:04,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference
[2023-06-18 19:17:06,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:17:06,262] [INFO] Task started: Prodigal
[2023-06-18 19:17:06,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg74db8434-0870-4fa0-9ab1-db89e0955f9a/GCA_018367705.1_ASM1836770v1_genomic.fna.gz | prodigal -d GCA_018367705.1_ASM1836770v1_genomic.fna/cds.fna -a GCA_018367705.1_ASM1836770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:17:09,453] [INFO] Task succeeded: Prodigal
[2023-06-18 19:17:09,454] [INFO] Task started: HMMsearch
[2023-06-18 19:17:09,454] [INFO] Running command: hmmsearch --tblout GCA_018367705.1_ASM1836770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference/reference_markers.hmm GCA_018367705.1_ASM1836770v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:17:09,760] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:17:09,761] [INFO] Found 6/6 markers.
[2023-06-18 19:17:09,801] [INFO] Query marker FASTA was written to GCA_018367705.1_ASM1836770v1_genomic.fna/markers.fasta
[2023-06-18 19:17:09,802] [INFO] Task started: Blastn
[2023-06-18 19:17:09,802] [INFO] Running command: blastn -query GCA_018367705.1_ASM1836770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference/reference_markers.fasta -out GCA_018367705.1_ASM1836770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:10,550] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:10,554] [INFO] Selected 16 target genomes.
[2023-06-18 19:17:10,555] [INFO] Target genome list was writen to GCA_018367705.1_ASM1836770v1_genomic.fna/target_genomes.txt
[2023-06-18 19:17:10,557] [INFO] Task started: fastANI
[2023-06-18 19:17:10,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg74db8434-0870-4fa0-9ab1-db89e0955f9a/GCA_018367705.1_ASM1836770v1_genomic.fna.gz --refList GCA_018367705.1_ASM1836770v1_genomic.fna/target_genomes.txt --output GCA_018367705.1_ASM1836770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:17:16,538] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:16,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:17:16,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:17:16,543] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 19:17:16,544] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 19:17:16,544] [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
Finegoldia magna	strain=DSM 20470	GCA_003182075.1	1260	1260	suspected-type	True	96.5999	442	490	95	conclusive
Finegoldia magna	strain=FDAARGOS_1593	GCA_020731325.1	1260	1260	suspected-type	True	96.5609	431	490	95	conclusive
--------------------------------------------------------------------------------
[2023-06-18 19:17:16,545] [INFO] DFAST Taxonomy check result was written to GCA_018367705.1_ASM1836770v1_genomic.fna/tc_result.tsv
[2023-06-18 19:17:16,546] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:17:16,546] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:17:16,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference/checkm_data
[2023-06-18 19:17:16,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:17:16,579] [INFO] Task started: CheckM
[2023-06-18 19:17:16,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018367705.1_ASM1836770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018367705.1_ASM1836770v1_genomic.fna/checkm_input GCA_018367705.1_ASM1836770v1_genomic.fna/checkm_result
[2023-06-18 19:17:34,987] [INFO] Task succeeded: CheckM
[2023-06-18 19:17:34,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:17:35,022] [INFO] ===== Completeness check finished =====
[2023-06-18 19:17:35,023] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:17:35,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018367705.1_ASM1836770v1_genomic.fna/markers.fasta)
[2023-06-18 19:17:35,024] [INFO] Task started: Blastn
[2023-06-18 19:17:35,024] [INFO] Running command: blastn -query GCA_018367705.1_ASM1836770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52eaf9f3-e387-4840-97ee-0d7e2b07ffc6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018367705.1_ASM1836770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:17:35,891] [INFO] Task succeeded: Blastn
[2023-06-18 19:17:35,900] [INFO] Selected 6 target genomes.
[2023-06-18 19:17:35,901] [INFO] Target genome list was writen to GCA_018367705.1_ASM1836770v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:17:35,906] [INFO] Task started: fastANI
[2023-06-18 19:17:35,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg74db8434-0870-4fa0-9ab1-db89e0955f9a/GCA_018367705.1_ASM1836770v1_genomic.fna.gz --refList GCA_018367705.1_ASM1836770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018367705.1_ASM1836770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:17:38,727] [INFO] Task succeeded: fastANI
[2023-06-18 19:17:38,737] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:17:38,738] [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
GCF_003182075.1	s__Finegoldia magna	96.5999	442	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	96.40	95.72	0.86	0.79	17	conclusive
GCF_000159695.1	s__Finegoldia magna_F	94.264	440	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	95.41	95.07	0.87	0.83	5	-
GCA_018371055.1	s__Finegoldia magna_I	93.1851	303	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766215.1	s__Finegoldia sp900766215	91.9972	413	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589545.1	s__Finegoldia sp910589545	91.5142	427	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010185.1	s__Finegoldia magna_H	91.012	446	490	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	97.29	95.99	0.88	0.82	13	-
--------------------------------------------------------------------------------
[2023-06-18 19:17:38,747] [INFO] GTDB search result was written to GCA_018367705.1_ASM1836770v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:17:38,751] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:17:38,756] [INFO] DFAST_QC result json was written to GCA_018367705.1_ASM1836770v1_genomic.fna/dqc_result.json
[2023-06-18 19:17:38,757] [INFO] DFAST_QC completed!
[2023-06-18 19:17:38,757] [INFO] Total running time: 0h0m34s