[2024-01-24 12:29:21,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:21,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:21,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference
[2024-01-24 12:29:22,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:22,968] [INFO] Task started: Prodigal
[2024-01-24 12:29:22,968] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b4e3419-5726-41b4-95c3-e841c7b7994a/GCF_002216005.1_ASM221600v1_genomic.fna.gz | prodigal -d GCF_002216005.1_ASM221600v1_genomic.fna/cds.fna -a GCF_002216005.1_ASM221600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:26,919] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:26,920] [INFO] Task started: HMMsearch
[2024-01-24 12:29:26,920] [INFO] Running command: hmmsearch --tblout GCF_002216005.1_ASM221600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference/reference_markers.hmm GCF_002216005.1_ASM221600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:27,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:27,160] [INFO] Found 6/6 markers.
[2024-01-24 12:29:27,190] [INFO] Query marker FASTA was written to GCF_002216005.1_ASM221600v1_genomic.fna/markers.fasta
[2024-01-24 12:29:27,190] [INFO] Task started: Blastn
[2024-01-24 12:29:27,190] [INFO] Running command: blastn -query GCF_002216005.1_ASM221600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference/reference_markers.fasta -out GCF_002216005.1_ASM221600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:27,760] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:27,763] [INFO] Selected 20 target genomes.
[2024-01-24 12:29:27,763] [INFO] Target genome list was writen to GCF_002216005.1_ASM221600v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:27,780] [INFO] Task started: fastANI
[2024-01-24 12:29:27,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4e3419-5726-41b4-95c3-e841c7b7994a/GCF_002216005.1_ASM221600v1_genomic.fna.gz --refList GCF_002216005.1_ASM221600v1_genomic.fna/target_genomes.txt --output GCF_002216005.1_ASM221600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:37,547] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:37,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:37,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:37,554] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:37,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:37,554] [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
Natranaerobius trueperi	strain=DSM 18760	GCA_002216005.1	759412	759412	type	True	100.0	835	840	95	conclusive
Natranaerobius thermophilus	strain=JW/NM-WN-LF	GCA_000020005.1	375929	375929	type	True	77.8717	108	840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:37,556] [INFO] DFAST Taxonomy check result was written to GCF_002216005.1_ASM221600v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:37,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:37,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:37,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference/checkm_data
[2024-01-24 12:29:37,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:37,585] [INFO] Task started: CheckM
[2024-01-24 12:29:37,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002216005.1_ASM221600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002216005.1_ASM221600v1_genomic.fna/checkm_input GCF_002216005.1_ASM221600v1_genomic.fna/checkm_result
[2024-01-24 12:29:57,194] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:57,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:57,217] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:57,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:57,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002216005.1_ASM221600v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:57,219] [INFO] Task started: Blastn
[2024-01-24 12:29:57,219] [INFO] Running command: blastn -query GCF_002216005.1_ASM221600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d6bde12-cc10-408e-a472-04f38c16fd2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002216005.1_ASM221600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:58,048] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:58,052] [INFO] Selected 21 target genomes.
[2024-01-24 12:29:58,052] [INFO] Target genome list was writen to GCF_002216005.1_ASM221600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:58,111] [INFO] Task started: fastANI
[2024-01-24 12:29:58,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b4e3419-5726-41b4-95c3-e841c7b7994a/GCF_002216005.1_ASM221600v1_genomic.fna.gz --refList GCF_002216005.1_ASM221600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002216005.1_ASM221600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:06,719] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:06,725] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:06,725] [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_002216005.1	s__Natranaerobius_A trueperi	100.0	835	840	d__Bacteria;p__Firmicutes_D;c__Natranaerobiia;o__Natranaerobiales;f__Natranaerobiaceae;g__Natranaerobius_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000020005.1	s__Natranaerobius thermophilus	77.9589	109	840	d__Bacteria;p__Firmicutes_D;c__Natranaerobiia;o__Natranaerobiales;f__Natranaerobiaceae;g__Natranaerobius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:06,727] [INFO] GTDB search result was written to GCF_002216005.1_ASM221600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:06,728] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:06,730] [INFO] DFAST_QC result json was written to GCF_002216005.1_ASM221600v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:06,730] [INFO] DFAST_QC completed!
[2024-01-24 12:30:06,730] [INFO] Total running time: 0h0m45s