[2023-06-17 01:07:53,215] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:07:53,218] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:07:53,218] [INFO] DQC Reference Directory: /var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference
[2023-06-17 01:07:54,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:07:54,809] [INFO] Task started: Prodigal
[2023-06-17 01:07:54,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg60e546bb-da64-4b86-bea4-246cf50115c1/GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna.gz | prodigal -d GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/cds.fna -a GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:08:08,518] [INFO] Task succeeded: Prodigal
[2023-06-17 01:08:08,519] [INFO] Task started: HMMsearch
[2023-06-17 01:08:08,519] [INFO] Running command: hmmsearch --tblout GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference/reference_markers.hmm GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:08:08,762] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:08:08,763] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60e546bb-da64-4b86-bea4-246cf50115c1/GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna.gz]
[2023-06-17 01:08:08,811] [INFO] Query marker FASTA was written to GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/markers.fasta
[2023-06-17 01:08:08,812] [INFO] Task started: Blastn
[2023-06-17 01:08:08,812] [INFO] Running command: blastn -query GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference/reference_markers.fasta -out GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:09,459] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:09,462] [INFO] Selected 23 target genomes.
[2023-06-17 01:08:09,463] [INFO] Target genome list was writen to GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/target_genomes.txt
[2023-06-17 01:08:09,481] [INFO] Task started: fastANI
[2023-06-17 01:08:09,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e546bb-da64-4b86-bea4-246cf50115c1/GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna.gz --refList GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/target_genomes.txt --output GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:08:26,482] [INFO] Task succeeded: fastANI
[2023-06-17 01:08:26,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:08:26,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:08:26,486] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:08:26,486] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:08:26,486] [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
--------------------------------------------------------------------------------
[2023-06-17 01:08:26,489] [INFO] DFAST Taxonomy check result was written to GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/tc_result.tsv
[2023-06-17 01:08:26,489] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:08:26,490] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:08:26,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference/checkm_data
[2023-06-17 01:08:26,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:08:26,529] [INFO] Task started: CheckM
[2023-06-17 01:08:26,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/checkm_input GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/checkm_result
[2023-06-17 01:09:10,069] [INFO] Task succeeded: CheckM
[2023-06-17 01:09:10,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 01:09:10,095] [INFO] ===== Completeness check finished =====
[2023-06-17 01:09:10,095] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:09:10,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/markers.fasta)
[2023-06-17 01:09:10,096] [INFO] Task started: Blastn
[2023-06-17 01:09:10,096] [INFO] Running command: blastn -query GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf19037b7-d1e3-40e8-84db-47daa6422ff6/dqc_reference/reference_markers_gtdb.fasta -out GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:09:10,972] [INFO] Task succeeded: Blastn
[2023-06-17 01:09:10,977] [INFO] Selected 22 target genomes.
[2023-06-17 01:09:10,977] [INFO] Target genome list was writen to GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:09:11,035] [INFO] Task started: fastANI
[2023-06-17 01:09:11,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e546bb-da64-4b86-bea4-246cf50115c1/GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna.gz --refList GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/target_genomes_gtdb.txt --output GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:09:21,880] [INFO] Task succeeded: fastANI
[2023-06-17 01:09:21,885] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:09:21,885] [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_002336485.1	s__SHAN690 sp002336485	99.7988	794	835	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Salibacteraceae;g__SHAN690	95.0	99.81	99.70	0.91	0.80	7	conclusive
--------------------------------------------------------------------------------
[2023-06-17 01:09:21,887] [INFO] GTDB search result was written to GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:09:21,888] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:09:21,890] [INFO] DFAST_QC result json was written to GCA_905479185.1_0.2_20180522_Bin_26_1_genomic.fna/dqc_result.json
[2023-06-17 01:09:21,890] [INFO] DFAST_QC completed!
[2023-06-17 01:09:21,890] [INFO] Total running time: 0h1m29s