[2023-06-28 04:58:51,908] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:58:51,917] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:58:51,917] [INFO] DQC Reference Directory: /var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference
[2023-06-28 04:58:53,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:58:53,204] [INFO] Task started: Prodigal
[2023-06-28 04:58:53,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg028ee64f-3732-447f-8963-3e35645841c5/GCA_944362535.1_BRZ_NT_bin32_genomic.fna.gz | prodigal -d GCA_944362535.1_BRZ_NT_bin32_genomic.fna/cds.fna -a GCA_944362535.1_BRZ_NT_bin32_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:58:57,637] [INFO] Task succeeded: Prodigal
[2023-06-28 04:58:57,637] [INFO] Task started: HMMsearch
[2023-06-28 04:58:57,637] [INFO] Running command: hmmsearch --tblout GCA_944362535.1_BRZ_NT_bin32_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference/reference_markers.hmm GCA_944362535.1_BRZ_NT_bin32_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:58:57,886] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:58:57,887] [INFO] Found 6/6 markers.
[2023-06-28 04:58:57,904] [INFO] Query marker FASTA was written to GCA_944362535.1_BRZ_NT_bin32_genomic.fna/markers.fasta
[2023-06-28 04:58:57,904] [INFO] Task started: Blastn
[2023-06-28 04:58:57,904] [INFO] Running command: blastn -query GCA_944362535.1_BRZ_NT_bin32_genomic.fna/markers.fasta -db /var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference/reference_markers.fasta -out GCA_944362535.1_BRZ_NT_bin32_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:58:58,543] [INFO] Task succeeded: Blastn
[2023-06-28 04:58:58,547] [INFO] Selected 20 target genomes.
[2023-06-28 04:58:58,547] [INFO] Target genome list was writen to GCA_944362535.1_BRZ_NT_bin32_genomic.fna/target_genomes.txt
[2023-06-28 04:58:58,551] [INFO] Task started: fastANI
[2023-06-28 04:58:58,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg028ee64f-3732-447f-8963-3e35645841c5/GCA_944362535.1_BRZ_NT_bin32_genomic.fna.gz --refList GCA_944362535.1_BRZ_NT_bin32_genomic.fna/target_genomes.txt --output GCA_944362535.1_BRZ_NT_bin32_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:59:09,828] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:09,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:59:09,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:59:09,830] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:59:09,831] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:59:09,831] [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
--------------------------------------------------------------------------------
[2023-06-28 04:59:09,833] [INFO] DFAST Taxonomy check result was written to GCA_944362535.1_BRZ_NT_bin32_genomic.fna/tc_result.tsv
[2023-06-28 04:59:09,834] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:59:09,834] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:59:09,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference/checkm_data
[2023-06-28 04:59:09,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:59:09,858] [INFO] Task started: CheckM
[2023-06-28 04:59:09,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944362535.1_BRZ_NT_bin32_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944362535.1_BRZ_NT_bin32_genomic.fna/checkm_input GCA_944362535.1_BRZ_NT_bin32_genomic.fna/checkm_result
[2023-06-28 04:59:30,349] [INFO] Task succeeded: CheckM
[2023-06-28 04:59:30,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:59:30,374] [INFO] ===== Completeness check finished =====
[2023-06-28 04:59:30,374] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:59:30,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944362535.1_BRZ_NT_bin32_genomic.fna/markers.fasta)
[2023-06-28 04:59:30,375] [INFO] Task started: Blastn
[2023-06-28 04:59:30,375] [INFO] Running command: blastn -query GCA_944362535.1_BRZ_NT_bin32_genomic.fna/markers.fasta -db /var/lib/cwl/stgca736345-4a11-403b-be9c-75cf8b9ad857/dqc_reference/reference_markers_gtdb.fasta -out GCA_944362535.1_BRZ_NT_bin32_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:31,196] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:31,201] [INFO] Selected 27 target genomes.
[2023-06-28 04:59:31,202] [INFO] Target genome list was writen to GCA_944362535.1_BRZ_NT_bin32_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:59:31,224] [INFO] Task started: fastANI
[2023-06-28 04:59:31,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg028ee64f-3732-447f-8963-3e35645841c5/GCA_944362535.1_BRZ_NT_bin32_genomic.fna.gz --refList GCA_944362535.1_BRZ_NT_bin32_genomic.fna/target_genomes_gtdb.txt --output GCA_944362535.1_BRZ_NT_bin32_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:59:41,424] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:41,433] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:59:41,433] [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_900553555.1	s__UMGS1795 sp900553555	98.3377	236	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__UMGS1795	95.0	98.45	97.89	0.84	0.74	5	conclusive
GCA_900761165.1	s__UMGS1795 sp900761165	79.9328	243	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__UMGS1795	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555125.1	s__UMGS1795 sp900555125	77.2102	89	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-552;g__UMGS1795	95.0	97.98	97.70	0.89	0.82	4	-
--------------------------------------------------------------------------------
[2023-06-28 04:59:41,435] [INFO] GTDB search result was written to GCA_944362535.1_BRZ_NT_bin32_genomic.fna/result_gtdb.tsv
[2023-06-28 04:59:41,436] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:59:41,438] [INFO] DFAST_QC result json was written to GCA_944362535.1_BRZ_NT_bin32_genomic.fna/dqc_result.json
[2023-06-28 04:59:41,438] [INFO] DFAST_QC completed!
[2023-06-28 04:59:41,438] [INFO] Total running time: 0h0m50s