[2024-01-24 13:46:01,900] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference
[2024-01-24 13:46:03,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:03,322] [INFO] Task started: Prodigal
[2024-01-24 13:46:03,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg1373cf9c-5d88-414a-b45a-db24614b678c/GCF_000430605.1_ASM43060v1_genomic.fna.gz | prodigal -d GCF_000430605.1_ASM43060v1_genomic.fna/cds.fna -a GCF_000430605.1_ASM43060v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:12,538] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:12,538] [INFO] Task started: HMMsearch
[2024-01-24 13:46:12,538] [INFO] Running command: hmmsearch --tblout GCF_000430605.1_ASM43060v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference/reference_markers.hmm GCF_000430605.1_ASM43060v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:12,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:12,832] [INFO] Found 6/6 markers.
[2024-01-24 13:46:12,865] [INFO] Query marker FASTA was written to GCF_000430605.1_ASM43060v1_genomic.fna/markers.fasta
[2024-01-24 13:46:12,865] [INFO] Task started: Blastn
[2024-01-24 13:46:12,865] [INFO] Running command: blastn -query GCF_000430605.1_ASM43060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference/reference_markers.fasta -out GCF_000430605.1_ASM43060v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:13,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:13,450] [INFO] Selected 21 target genomes.
[2024-01-24 13:46:13,450] [INFO] Target genome list was writen to GCF_000430605.1_ASM43060v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:13,461] [INFO] Task started: fastANI
[2024-01-24 13:46:13,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg1373cf9c-5d88-414a-b45a-db24614b678c/GCF_000430605.1_ASM43060v1_genomic.fna.gz --refList GCF_000430605.1_ASM43060v1_genomic.fna/target_genomes.txt --output GCF_000430605.1_ASM43060v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:25,545] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:25,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:25,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:25,547] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:25,547] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:46:25,547] [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
--------------------------------------------------------------------------------
[2024-01-24 13:46:25,549] [INFO] DFAST Taxonomy check result was written to GCF_000430605.1_ASM43060v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:25,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:25,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:25,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference/checkm_data
[2024-01-24 13:46:25,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:25,588] [INFO] Task started: CheckM
[2024-01-24 13:46:25,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430605.1_ASM43060v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430605.1_ASM43060v1_genomic.fna/checkm_input GCF_000430605.1_ASM43060v1_genomic.fna/checkm_result
[2024-01-24 13:46:57,367] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:57,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:57,388] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:57,389] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:57,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430605.1_ASM43060v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:57,390] [INFO] Task started: Blastn
[2024-01-24 13:46:57,390] [INFO] Running command: blastn -query GCF_000430605.1_ASM43060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c914b85-c01c-41b4-91c3-3831b0d22a4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430605.1_ASM43060v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,256] [INFO] Selected 20 target genomes.
[2024-01-24 13:46:58,257] [INFO] Target genome list was writen to GCF_000430605.1_ASM43060v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:58,308] [INFO] Task started: fastANI
[2024-01-24 13:46:58,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg1373cf9c-5d88-414a-b45a-db24614b678c/GCF_000430605.1_ASM43060v1_genomic.fna.gz --refList GCF_000430605.1_ASM43060v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430605.1_ASM43060v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:09,980] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:09,984] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:09,985] [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_000374545.1	s__Anaeromusa acidaminophila	97.604	915	1100	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Anaeromusales;f__Anaeromusaceae;g__Anaeromusa	95.0	97.64	97.64	0.83	0.83	2	conclusive
GCA_009929485.1	s__Anaeromusa sp009929485	88.7335	796	1100	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Anaeromusales;f__Anaeromusaceae;g__Anaeromusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,986] [INFO] GTDB search result was written to GCF_000430605.1_ASM43060v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:09,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:09,990] [INFO] DFAST_QC result json was written to GCF_000430605.1_ASM43060v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:09,990] [INFO] DFAST_QC completed!
[2024-01-24 13:47:09,990] [INFO] Total running time: 0h1m8s