[2023-06-05 09:25:22,368] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:25:22,385] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:25:22,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference
[2023-06-05 09:25:23,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:25:23,832] [INFO] Task started: Prodigal
[2023-06-05 09:25:23,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf84025f-fd59-4ea2-ac01-02f366cf340c/GCA_001821305.1_ASM182130v1_genomic.fna.gz | prodigal -d GCA_001821305.1_ASM182130v1_genomic.fna/cds.fna -a GCA_001821305.1_ASM182130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:25:27,646] [INFO] Task succeeded: Prodigal
[2023-06-05 09:25:27,647] [INFO] Task started: HMMsearch
[2023-06-05 09:25:27,647] [INFO] Running command: hmmsearch --tblout GCA_001821305.1_ASM182130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference/reference_markers.hmm GCA_001821305.1_ASM182130v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:25:27,854] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:25:27,855] [INFO] Found 6/6 markers.
[2023-06-05 09:25:27,869] [INFO] Query marker FASTA was written to GCA_001821305.1_ASM182130v1_genomic.fna/markers.fasta
[2023-06-05 09:25:27,870] [INFO] Task started: Blastn
[2023-06-05 09:25:27,870] [INFO] Running command: blastn -query GCA_001821305.1_ASM182130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference/reference_markers.fasta -out GCA_001821305.1_ASM182130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:28,448] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:28,453] [INFO] Selected 15 target genomes.
[2023-06-05 09:25:28,454] [INFO] Target genome list was writen to GCA_001821305.1_ASM182130v1_genomic.fna/target_genomes.txt
[2023-06-05 09:25:28,457] [INFO] Task started: fastANI
[2023-06-05 09:25:28,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf84025f-fd59-4ea2-ac01-02f366cf340c/GCA_001821305.1_ASM182130v1_genomic.fna.gz --refList GCA_001821305.1_ASM182130v1_genomic.fna/target_genomes.txt --output GCA_001821305.1_ASM182130v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:25:36,807] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:36,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:25:36,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:25:36,810] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:25:36,811] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 09:25:36,811] [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
--------------------------------------------------------------------------------
[2023-06-05 09:25:36,813] [INFO] DFAST Taxonomy check result was written to GCA_001821305.1_ASM182130v1_genomic.fna/tc_result.tsv
[2023-06-05 09:25:36,814] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:25:36,814] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:25:36,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference/checkm_data
[2023-06-05 09:25:36,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:25:36,833] [INFO] Task started: CheckM
[2023-06-05 09:25:36,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001821305.1_ASM182130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001821305.1_ASM182130v1_genomic.fna/checkm_input GCA_001821305.1_ASM182130v1_genomic.fna/checkm_result
[2023-06-05 09:25:55,186] [INFO] Task succeeded: CheckM
[2023-06-05 09:25:55,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.81%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:25:55,209] [INFO] ===== Completeness check finished =====
[2023-06-05 09:25:55,209] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:25:55,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001821305.1_ASM182130v1_genomic.fna/markers.fasta)
[2023-06-05 09:25:55,210] [INFO] Task started: Blastn
[2023-06-05 09:25:55,210] [INFO] Running command: blastn -query GCA_001821305.1_ASM182130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50396a63-3e5d-4822-bacb-4eaf7932e3d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_001821305.1_ASM182130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:25:55,977] [INFO] Task succeeded: Blastn
[2023-06-05 09:25:55,981] [INFO] Selected 15 target genomes.
[2023-06-05 09:25:55,981] [INFO] Target genome list was writen to GCA_001821305.1_ASM182130v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:25:55,988] [INFO] Task started: fastANI
[2023-06-05 09:25:55,989] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf84025f-fd59-4ea2-ac01-02f366cf340c/GCA_001821305.1_ASM182130v1_genomic.fna.gz --refList GCA_001821305.1_ASM182130v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001821305.1_ASM182130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:25:58,563] [INFO] Task succeeded: fastANI
[2023-06-05 09:25:58,570] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:25:58,570] [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_001821135.1	s__2-02-FULL-48-16 sp001821135	99.9015	196	226	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA10002;g__2-02-FULL-48-16	95.0	99.96	99.95	0.96	0.93	5	conclusive
GCA_007376285.1	s__2-02-FULL-48-16 sp007376285	78.7461	86	226	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA10002;g__2-02-FULL-48-16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:25:58,572] [INFO] GTDB search result was written to GCA_001821305.1_ASM182130v1_genomic.fna/result_gtdb.tsv
[2023-06-05 09:25:58,573] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:25:58,576] [INFO] DFAST_QC result json was written to GCA_001821305.1_ASM182130v1_genomic.fna/dqc_result.json
[2023-06-05 09:25:58,576] [INFO] DFAST_QC completed!
[2023-06-05 09:25:58,576] [INFO] Total running time: 0h0m36s