[2023-06-28 05:09:05,930] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:09:05,933] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:09:05,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference
[2023-06-28 05:09:07,357] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:09:07,358] [INFO] Task started: Prodigal
[2023-06-28 05:09:07,358] [INFO] Running command: gunzip -c /var/lib/cwl/stgc764a8d2-b1c5-4826-9243-cb5f0cf1aed9/GCA_017438595.1_ASM1743859v1_genomic.fna.gz | prodigal -d GCA_017438595.1_ASM1743859v1_genomic.fna/cds.fna -a GCA_017438595.1_ASM1743859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:09:10,119] [INFO] Task succeeded: Prodigal
[2023-06-28 05:09:10,119] [INFO] Task started: HMMsearch
[2023-06-28 05:09:10,119] [INFO] Running command: hmmsearch --tblout GCA_017438595.1_ASM1743859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference/reference_markers.hmm GCA_017438595.1_ASM1743859v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:09:10,349] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:09:10,351] [INFO] Found 6/6 markers.
[2023-06-28 05:09:10,382] [INFO] Query marker FASTA was written to GCA_017438595.1_ASM1743859v1_genomic.fna/markers.fasta
[2023-06-28 05:09:10,383] [INFO] Task started: Blastn
[2023-06-28 05:09:10,383] [INFO] Running command: blastn -query GCA_017438595.1_ASM1743859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference/reference_markers.fasta -out GCA_017438595.1_ASM1743859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:09:11,031] [INFO] Task succeeded: Blastn
[2023-06-28 05:09:11,035] [INFO] Selected 21 target genomes.
[2023-06-28 05:09:11,036] [INFO] Target genome list was writen to GCA_017438595.1_ASM1743859v1_genomic.fna/target_genomes.txt
[2023-06-28 05:09:11,044] [INFO] Task started: fastANI
[2023-06-28 05:09:11,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgc764a8d2-b1c5-4826-9243-cb5f0cf1aed9/GCA_017438595.1_ASM1743859v1_genomic.fna.gz --refList GCA_017438595.1_ASM1743859v1_genomic.fna/target_genomes.txt --output GCA_017438595.1_ASM1743859v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:09:21,250] [INFO] Task succeeded: fastANI
[2023-06-28 05:09:21,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:09:21,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:09:21,252] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:09:21,252] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:09:21,252] [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 05:09:21,254] [INFO] DFAST Taxonomy check result was written to GCA_017438595.1_ASM1743859v1_genomic.fna/tc_result.tsv
[2023-06-28 05:09:21,255] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:09:21,255] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:09:21,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference/checkm_data
[2023-06-28 05:09:21,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:09:21,278] [INFO] Task started: CheckM
[2023-06-28 05:09:21,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017438595.1_ASM1743859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017438595.1_ASM1743859v1_genomic.fna/checkm_input GCA_017438595.1_ASM1743859v1_genomic.fna/checkm_result
[2023-06-28 05:09:37,470] [INFO] Task succeeded: CheckM
[2023-06-28 05:09:37,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:09:37,490] [INFO] ===== Completeness check finished =====
[2023-06-28 05:09:37,491] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:09:37,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017438595.1_ASM1743859v1_genomic.fna/markers.fasta)
[2023-06-28 05:09:37,492] [INFO] Task started: Blastn
[2023-06-28 05:09:37,492] [INFO] Running command: blastn -query GCA_017438595.1_ASM1743859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb75d87ae-9480-4a5f-af8b-5a04173c73f9/dqc_reference/reference_markers_gtdb.fasta -out GCA_017438595.1_ASM1743859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:09:38,314] [INFO] Task succeeded: Blastn
[2023-06-28 05:09:38,317] [INFO] Selected 27 target genomes.
[2023-06-28 05:09:38,318] [INFO] Target genome list was writen to GCA_017438595.1_ASM1743859v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:09:38,338] [INFO] Task started: fastANI
[2023-06-28 05:09:38,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgc764a8d2-b1c5-4826-9243-cb5f0cf1aed9/GCA_017438595.1_ASM1743859v1_genomic.fna.gz --refList GCA_017438595.1_ASM1743859v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017438595.1_ASM1743859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:09:49,470] [INFO] Task succeeded: fastANI
[2023-06-28 05:09:49,479] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:09:49,479] [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_017406485.1	s__CAG-41 sp017406485	96.5977	202	238	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001941225.1	s__CAG-41 sp001941225	77.6288	68	238	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579415.1	s__CAG-41 sp910579415	77.1746	53	238	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1381;f__UBA1381;g__CAG-41	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:09:49,481] [INFO] GTDB search result was written to GCA_017438595.1_ASM1743859v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:09:49,482] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:09:49,485] [INFO] DFAST_QC result json was written to GCA_017438595.1_ASM1743859v1_genomic.fna/dqc_result.json
[2023-06-28 05:09:49,486] [INFO] DFAST_QC completed!
[2023-06-28 05:09:49,486] [INFO] Total running time: 0h0m44s