[2023-06-08 18:15:26,049] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:15:26,051] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:15:26,051] [INFO] DQC Reference Directory: /var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference
[2023-06-08 18:15:27,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:15:27,227] [INFO] Task started: Prodigal
[2023-06-08 18:15:27,227] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbfa660b-1b82-4ea0-941d-e7c89e64042e/GCA_902620845.1_AG-920-M15_genomic.fna.gz | prodigal -d GCA_902620845.1_AG-920-M15_genomic.fna/cds.fna -a GCA_902620845.1_AG-920-M15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:15:28,365] [INFO] Task succeeded: Prodigal
[2023-06-08 18:15:28,365] [INFO] Task started: HMMsearch
[2023-06-08 18:15:28,366] [INFO] Running command: hmmsearch --tblout GCA_902620845.1_AG-920-M15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference/reference_markers.hmm GCA_902620845.1_AG-920-M15_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:15:28,531] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:15:28,532] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgfbfa660b-1b82-4ea0-941d-e7c89e64042e/GCA_902620845.1_AG-920-M15_genomic.fna.gz]
[2023-06-08 18:15:28,546] [INFO] Query marker FASTA was written to GCA_902620845.1_AG-920-M15_genomic.fna/markers.fasta
[2023-06-08 18:15:28,547] [INFO] Task started: Blastn
[2023-06-08 18:15:28,547] [INFO] Running command: blastn -query GCA_902620845.1_AG-920-M15_genomic.fna/markers.fasta -db /var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference/reference_markers.fasta -out GCA_902620845.1_AG-920-M15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:15:29,054] [INFO] Task succeeded: Blastn
[2023-06-08 18:15:29,058] [INFO] Selected 10 target genomes.
[2023-06-08 18:15:29,058] [INFO] Target genome list was writen to GCA_902620845.1_AG-920-M15_genomic.fna/target_genomes.txt
[2023-06-08 18:15:29,062] [INFO] Task started: fastANI
[2023-06-08 18:15:29,062] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbfa660b-1b82-4ea0-941d-e7c89e64042e/GCA_902620845.1_AG-920-M15_genomic.fna.gz --refList GCA_902620845.1_AG-920-M15_genomic.fna/target_genomes.txt --output GCA_902620845.1_AG-920-M15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:15:32,130] [INFO] Task succeeded: fastANI
[2023-06-08 18:15:32,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:15:32,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:15:32,133] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:15:32,133] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 18:15:32,134] [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
--------------------------------------------------------------------------------
[2023-06-08 18:15:32,136] [INFO] DFAST Taxonomy check result was written to GCA_902620845.1_AG-920-M15_genomic.fna/tc_result.tsv
[2023-06-08 18:15:32,137] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:15:32,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:15:32,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference/checkm_data
[2023-06-08 18:15:32,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:15:32,156] [INFO] Task started: CheckM
[2023-06-08 18:15:32,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902620845.1_AG-920-M15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902620845.1_AG-920-M15_genomic.fna/checkm_input GCA_902620845.1_AG-920-M15_genomic.fna/checkm_result
[2023-06-08 18:15:44,109] [INFO] Task succeeded: CheckM
[2023-06-08 18:15:44,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:15:44,134] [INFO] ===== Completeness check finished =====
[2023-06-08 18:15:44,134] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:15:44,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902620845.1_AG-920-M15_genomic.fna/markers.fasta)
[2023-06-08 18:15:44,135] [INFO] Task started: Blastn
[2023-06-08 18:15:44,135] [INFO] Running command: blastn -query GCA_902620845.1_AG-920-M15_genomic.fna/markers.fasta -db /var/lib/cwl/stg86a99a87-3992-4a04-bdb2-c5d23860d03c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902620845.1_AG-920-M15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:15:44,699] [INFO] Task succeeded: Blastn
[2023-06-08 18:15:44,704] [INFO] Selected 9 target genomes.
[2023-06-08 18:15:44,704] [INFO] Target genome list was writen to GCA_902620845.1_AG-920-M15_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:15:44,708] [INFO] Task started: fastANI
[2023-06-08 18:15:44,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbfa660b-1b82-4ea0-941d-e7c89e64042e/GCA_902620845.1_AG-920-M15_genomic.fna.gz --refList GCA_902620845.1_AG-920-M15_genomic.fna/target_genomes_gtdb.txt --output GCA_902620845.1_AG-920-M15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:15:46,362] [INFO] Task succeeded: fastANI
[2023-06-08 18:15:46,368] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:15:46,369] [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_902584815.1	s__CABYIR01 sp902584815	97.5944	147	214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CABYIR01	95.0	97.27	95.18	0.69	0.61	8	conclusive
GCA_902518955.1	s__CABYIR01 sp902518955	93.4743	149	214	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__CABYIR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 18:15:46,371] [INFO] GTDB search result was written to GCA_902620845.1_AG-920-M15_genomic.fna/result_gtdb.tsv
[2023-06-08 18:15:46,376] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:15:46,379] [INFO] DFAST_QC result json was written to GCA_902620845.1_AG-920-M15_genomic.fna/dqc_result.json
[2023-06-08 18:15:46,379] [INFO] DFAST_QC completed!
[2023-06-08 18:15:46,379] [INFO] Total running time: 0h0m20s