[2023-06-16 20:19:15,001] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:19:15,006] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:19:15,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference
[2023-06-16 20:19:16,773] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:19:16,774] [INFO] Task started: Prodigal
[2023-06-16 20:19:16,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8f7e220-4fea-410a-95ae-70a1877f11f9/GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna.gz | prodigal -d GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/cds.fna -a GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:19:19,274] [INFO] Task succeeded: Prodigal
[2023-06-16 20:19:19,274] [INFO] Task started: HMMsearch
[2023-06-16 20:19:19,274] [INFO] Running command: hmmsearch --tblout GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference/reference_markers.hmm GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:19:19,453] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:19:19,454] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd8f7e220-4fea-410a-95ae-70a1877f11f9/GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna.gz]
[2023-06-16 20:19:19,471] [INFO] Query marker FASTA was written to GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/markers.fasta
[2023-06-16 20:19:19,472] [INFO] Task started: Blastn
[2023-06-16 20:19:19,472] [INFO] Running command: blastn -query GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference/reference_markers.fasta -out GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:19:20,679] [INFO] Task succeeded: Blastn
[2023-06-16 20:19:20,685] [INFO] Selected 10 target genomes.
[2023-06-16 20:19:20,686] [INFO] Target genome list was writen to GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/target_genomes.txt
[2023-06-16 20:19:20,686] [INFO] Task started: fastANI
[2023-06-16 20:19:20,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8f7e220-4fea-410a-95ae-70a1877f11f9/GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna.gz --refList GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/target_genomes.txt --output GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:19:27,573] [INFO] Task succeeded: fastANI
[2023-06-16 20:19:27,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:19:27,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:19:27,575] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:19:27,575] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 20:19:27,575] [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
--------------------------------------------------------------------------------
[2023-06-16 20:19:27,576] [INFO] DFAST Taxonomy check result was written to GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/tc_result.tsv
[2023-06-16 20:19:27,578] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:19:27,578] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:19:27,578] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference/checkm_data
[2023-06-16 20:19:27,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:19:27,598] [INFO] Task started: CheckM
[2023-06-16 20:19:27,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/checkm_input GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/checkm_result
[2023-06-16 20:19:41,861] [INFO] Task succeeded: CheckM
[2023-06-16 20:19:41,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 5.73%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:19:41,891] [INFO] ===== Completeness check finished =====
[2023-06-16 20:19:41,892] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:19:41,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/markers.fasta)
[2023-06-16 20:19:41,892] [INFO] Task started: Blastn
[2023-06-16 20:19:41,892] [INFO] Running command: blastn -query GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/markers.fasta -db /var/lib/cwl/stg288bf982-e6a8-46b4-9aa6-e95963c65ed3/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:19:42,388] [INFO] Task succeeded: Blastn
[2023-06-16 20:19:42,391] [INFO] Selected 7 target genomes.
[2023-06-16 20:19:42,391] [INFO] Target genome list was writen to GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:19:42,395] [INFO] Task started: fastANI
[2023-06-16 20:19:42,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8f7e220-4fea-410a-95ae-70a1877f11f9/GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna.gz --refList GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/target_genomes_gtdb.txt --output GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:19:44,660] [INFO] Task succeeded: fastANI
[2023-06-16 20:19:44,664] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:19:44,664] [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_900767195.1	s__UBA7597 sp900767195	97.0038	134	172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900542935.1	s__UBA7597 sp900542935	84.7349	108	172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	98.09	97.76	0.86	0.81	5	-
GCA_002474405.1	s__UBA7597 sp002474405	82.6462	96	172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905203015.1	s__UBA7597 sp003448195	80.6723	67	172	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA7597	95.0	98.98	98.79	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2023-06-16 20:19:44,666] [INFO] GTDB search result was written to GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/result_gtdb.tsv
[2023-06-16 20:19:44,667] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:19:44,668] [INFO] DFAST_QC result json was written to GCA_905207565.1_ERR321619-mag-bin.20_genomic.fna/dqc_result.json
[2023-06-16 20:19:44,669] [INFO] DFAST_QC completed!
[2023-06-16 20:19:44,669] [INFO] Total running time: 0h0m30s