[2023-06-19 04:44:56,175] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:44:56,178] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:44:56,178] [INFO] DQC Reference Directory: /var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference
[2023-06-19 04:44:58,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:44:58,518] [INFO] Task started: Prodigal
[2023-06-19 04:44:58,518] [INFO] Running command: gunzip -c /var/lib/cwl/stga24e6d0c-4a12-418e-9fae-4d02940a9ddb/GCA_018062285.1_ASM1806228v1_genomic.fna.gz | prodigal -d GCA_018062285.1_ASM1806228v1_genomic.fna/cds.fna -a GCA_018062285.1_ASM1806228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:45:01,881] [INFO] Task succeeded: Prodigal
[2023-06-19 04:45:01,882] [INFO] Task started: HMMsearch
[2023-06-19 04:45:01,882] [INFO] Running command: hmmsearch --tblout GCA_018062285.1_ASM1806228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference/reference_markers.hmm GCA_018062285.1_ASM1806228v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:45:02,073] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:45:02,075] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga24e6d0c-4a12-418e-9fae-4d02940a9ddb/GCA_018062285.1_ASM1806228v1_genomic.fna.gz]
[2023-06-19 04:45:02,091] [INFO] Query marker FASTA was written to GCA_018062285.1_ASM1806228v1_genomic.fna/markers.fasta
[2023-06-19 04:45:02,092] [INFO] Task started: Blastn
[2023-06-19 04:45:02,092] [INFO] Running command: blastn -query GCA_018062285.1_ASM1806228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference/reference_markers.fasta -out GCA_018062285.1_ASM1806228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:45:04,596] [INFO] Task succeeded: Blastn
[2023-06-19 04:45:04,601] [INFO] Selected 16 target genomes.
[2023-06-19 04:45:04,602] [INFO] Target genome list was writen to GCA_018062285.1_ASM1806228v1_genomic.fna/target_genomes.txt
[2023-06-19 04:45:04,613] [INFO] Task started: fastANI
[2023-06-19 04:45:04,614] [INFO] Running command: fastANI --query /var/lib/cwl/stga24e6d0c-4a12-418e-9fae-4d02940a9ddb/GCA_018062285.1_ASM1806228v1_genomic.fna.gz --refList GCA_018062285.1_ASM1806228v1_genomic.fna/target_genomes.txt --output GCA_018062285.1_ASM1806228v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:45:13,098] [INFO] Task succeeded: fastANI
[2023-06-19 04:45:13,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:45:13,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:45:13,102] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:45:13,102] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:45:13,102] [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
--------------------------------------------------------------------------------
[2023-06-19 04:45:13,104] [INFO] DFAST Taxonomy check result was written to GCA_018062285.1_ASM1806228v1_genomic.fna/tc_result.tsv
[2023-06-19 04:45:13,105] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:45:13,106] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:45:13,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference/checkm_data
[2023-06-19 04:45:13,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:45:13,125] [INFO] Task started: CheckM
[2023-06-19 04:45:13,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018062285.1_ASM1806228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018062285.1_ASM1806228v1_genomic.fna/checkm_input GCA_018062285.1_ASM1806228v1_genomic.fna/checkm_result
[2023-06-19 04:45:31,794] [INFO] Task succeeded: CheckM
[2023-06-19 04:45:31,795] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:45:31,816] [INFO] ===== Completeness check finished =====
[2023-06-19 04:45:31,816] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:45:31,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018062285.1_ASM1806228v1_genomic.fna/markers.fasta)
[2023-06-19 04:45:31,817] [INFO] Task started: Blastn
[2023-06-19 04:45:31,817] [INFO] Running command: blastn -query GCA_018062285.1_ASM1806228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge58f6400-3da0-422b-9cf2-030c0f8e05a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018062285.1_ASM1806228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:45:32,649] [INFO] Task succeeded: Blastn
[2023-06-19 04:45:32,654] [INFO] Selected 17 target genomes.
[2023-06-19 04:45:32,654] [INFO] Target genome list was writen to GCA_018062285.1_ASM1806228v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:45:32,665] [INFO] Task started: fastANI
[2023-06-19 04:45:32,665] [INFO] Running command: fastANI --query /var/lib/cwl/stga24e6d0c-4a12-418e-9fae-4d02940a9ddb/GCA_018062285.1_ASM1806228v1_genomic.fna.gz --refList GCA_018062285.1_ASM1806228v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018062285.1_ASM1806228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:45:37,599] [INFO] Task succeeded: fastANI
[2023-06-19 04:45:37,603] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:45:37,604] [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_018062285.1	s__2-01-FULL-41-21 sp018062285	100.0	230	230	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__2-02-FULL-40-12;f__GWA2-44-9;g__2-01-FULL-41-21	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-19 04:45:37,606] [INFO] GTDB search result was written to GCA_018062285.1_ASM1806228v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:45:37,606] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:45:37,609] [INFO] DFAST_QC result json was written to GCA_018062285.1_ASM1806228v1_genomic.fna/dqc_result.json
[2023-06-19 04:45:37,609] [INFO] DFAST_QC completed!
[2023-06-19 04:45:37,609] [INFO] Total running time: 0h0m41s