[2024-01-24 12:13:23,638] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference
[2024-01-24 12:13:24,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:24,872] [INFO] Task started: Prodigal
[2024-01-24 12:13:24,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ad45db7-c58d-4783-8ae4-460fd1be600f/GCF_007993755.1_ASM799375v1_genomic.fna.gz | prodigal -d GCF_007993755.1_ASM799375v1_genomic.fna/cds.fna -a GCF_007993755.1_ASM799375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:44,361] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:44,362] [INFO] Task started: HMMsearch
[2024-01-24 12:13:44,362] [INFO] Running command: hmmsearch --tblout GCF_007993755.1_ASM799375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference/reference_markers.hmm GCF_007993755.1_ASM799375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:44,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:44,842] [INFO] Found 6/6 markers.
[2024-01-24 12:13:44,897] [INFO] Query marker FASTA was written to GCF_007993755.1_ASM799375v1_genomic.fna/markers.fasta
[2024-01-24 12:13:44,898] [INFO] Task started: Blastn
[2024-01-24 12:13:44,898] [INFO] Running command: blastn -query GCF_007993755.1_ASM799375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference/reference_markers.fasta -out GCF_007993755.1_ASM799375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:45,533] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:45,537] [INFO] Selected 25 target genomes.
[2024-01-24 12:13:45,538] [INFO] Target genome list was writen to GCF_007993755.1_ASM799375v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:45,547] [INFO] Task started: fastANI
[2024-01-24 12:13:45,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ad45db7-c58d-4783-8ae4-460fd1be600f/GCF_007993755.1_ASM799375v1_genomic.fna.gz --refList GCF_007993755.1_ASM799375v1_genomic.fna/target_genomes.txt --output GCF_007993755.1_ASM799375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:06,238] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:06,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:06,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:06,243] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:06,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:06,244] [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
Microvenator marinus	strain=V1718	GCA_007993755.1	2600177	2600177	type	True	100.0	1949	1949	95	conclusive
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	76.655	63	1949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:06,246] [INFO] DFAST Taxonomy check result was written to GCF_007993755.1_ASM799375v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:06,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:06,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:06,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference/checkm_data
[2024-01-24 12:14:06,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:06,305] [INFO] Task started: CheckM
[2024-01-24 12:14:06,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993755.1_ASM799375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993755.1_ASM799375v1_genomic.fna/checkm_input GCF_007993755.1_ASM799375v1_genomic.fna/checkm_result
[2024-01-24 12:15:05,380] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:05,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,417] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:05,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:05,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993755.1_ASM799375v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:05,419] [INFO] Task started: Blastn
[2024-01-24 12:15:05,419] [INFO] Running command: blastn -query GCF_007993755.1_ASM799375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd1733e4-4a32-41ce-81b0-abdbcb2eb1ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993755.1_ASM799375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:06,309] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:06,314] [INFO] Selected 29 target genomes.
[2024-01-24 12:15:06,315] [INFO] Target genome list was writen to GCF_007993755.1_ASM799375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:06,364] [INFO] Task started: fastANI
[2024-01-24 12:15:06,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ad45db7-c58d-4783-8ae4-460fd1be600f/GCF_007993755.1_ASM799375v1_genomic.fna.gz --refList GCF_007993755.1_ASM799375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993755.1_ASM799375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:31,678] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:31,681] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:31,681] [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_007993755.1	s__V1718 sp007993755	100.0	1949	1949	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__V1718	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007997015.1	s__Lujinxingia sp007997015	76.655	63	1949	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:31,683] [INFO] GTDB search result was written to GCF_007993755.1_ASM799375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:31,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:31,685] [INFO] DFAST_QC result json was written to GCF_007993755.1_ASM799375v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:31,685] [INFO] DFAST_QC completed!
[2024-01-24 12:15:31,686] [INFO] Total running time: 0h2m8s