[2023-06-26 22:36:49,653] [INFO] DFAST_QC pipeline started.
[2023-06-26 22:36:49,655] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 22:36:49,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference
[2023-06-26 22:36:51,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 22:36:51,241] [INFO] Task started: Prodigal
[2023-06-26 22:36:51,241] [INFO] Running command: gunzip -c /var/lib/cwl/stga73e3157-6fe9-46b3-89c8-d95caa0977e5/GCA_026710545.1_ASM2671054v1_genomic.fna.gz | prodigal -d GCA_026710545.1_ASM2671054v1_genomic.fna/cds.fna -a GCA_026710545.1_ASM2671054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 22:37:03,024] [INFO] Task succeeded: Prodigal
[2023-06-26 22:37:03,025] [INFO] Task started: HMMsearch
[2023-06-26 22:37:03,025] [INFO] Running command: hmmsearch --tblout GCA_026710545.1_ASM2671054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference/reference_markers.hmm GCA_026710545.1_ASM2671054v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 22:37:03,256] [INFO] Task succeeded: HMMsearch
[2023-06-26 22:37:03,258] [INFO] Found 6/6 markers.
[2023-06-26 22:37:03,304] [INFO] Query marker FASTA was written to GCA_026710545.1_ASM2671054v1_genomic.fna/markers.fasta
[2023-06-26 22:37:03,304] [INFO] Task started: Blastn
[2023-06-26 22:37:03,304] [INFO] Running command: blastn -query GCA_026710545.1_ASM2671054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference/reference_markers.fasta -out GCA_026710545.1_ASM2671054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:37:04,011] [INFO] Task succeeded: Blastn
[2023-06-26 22:37:04,015] [INFO] Selected 35 target genomes.
[2023-06-26 22:37:04,016] [INFO] Target genome list was writen to GCA_026710545.1_ASM2671054v1_genomic.fna/target_genomes.txt
[2023-06-26 22:37:04,035] [INFO] Task started: fastANI
[2023-06-26 22:37:04,036] [INFO] Running command: fastANI --query /var/lib/cwl/stga73e3157-6fe9-46b3-89c8-d95caa0977e5/GCA_026710545.1_ASM2671054v1_genomic.fna.gz --refList GCA_026710545.1_ASM2671054v1_genomic.fna/target_genomes.txt --output GCA_026710545.1_ASM2671054v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 22:37:29,688] [INFO] Task succeeded: fastANI
[2023-06-26 22:37:29,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 22:37:29,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 22:37:29,693] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 22:37:29,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 22:37:29,694] [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
Methylohalomonas lacus	strain=HMT 1	GCA_024808875.1	398773	398773	type	True	75.615	50	1408	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	75.0291	52	1408	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 22:37:29,703] [INFO] DFAST Taxonomy check result was written to GCA_026710545.1_ASM2671054v1_genomic.fna/tc_result.tsv
[2023-06-26 22:37:29,703] [INFO] ===== Taxonomy check completed =====
[2023-06-26 22:37:29,703] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 22:37:29,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference/checkm_data
[2023-06-26 22:37:29,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 22:37:29,748] [INFO] Task started: CheckM
[2023-06-26 22:37:29,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026710545.1_ASM2671054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026710545.1_ASM2671054v1_genomic.fna/checkm_input GCA_026710545.1_ASM2671054v1_genomic.fna/checkm_result
[2023-06-26 22:38:06,695] [INFO] Task succeeded: CheckM
[2023-06-26 22:38:06,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 22:38:06,733] [INFO] ===== Completeness check finished =====
[2023-06-26 22:38:06,733] [INFO] ===== Start GTDB Search =====
[2023-06-26 22:38:06,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026710545.1_ASM2671054v1_genomic.fna/markers.fasta)
[2023-06-26 22:38:06,733] [INFO] Task started: Blastn
[2023-06-26 22:38:06,734] [INFO] Running command: blastn -query GCA_026710545.1_ASM2671054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb00aaae-4d43-4c17-bbed-657c77eb4cdb/dqc_reference/reference_markers_gtdb.fasta -out GCA_026710545.1_ASM2671054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:38:07,903] [INFO] Task succeeded: Blastn
[2023-06-26 22:38:07,916] [INFO] Selected 30 target genomes.
[2023-06-26 22:38:07,917] [INFO] Target genome list was writen to GCA_026710545.1_ASM2671054v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 22:38:07,965] [INFO] Task started: fastANI
[2023-06-26 22:38:07,966] [INFO] Running command: fastANI --query /var/lib/cwl/stga73e3157-6fe9-46b3-89c8-d95caa0977e5/GCA_026710545.1_ASM2671054v1_genomic.fna.gz --refList GCA_026710545.1_ASM2671054v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026710545.1_ASM2671054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 22:38:27,030] [INFO] Task succeeded: fastANI
[2023-06-26 22:38:27,035] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 22:38:27,035] [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_009843675.1	s__JAAXHV01 sp009843675	82.1292	442	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__JAAXHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270695.1	s__JAAXHV01 sp012270695	81.9217	479	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__JAAXHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801865.1	s__2-02-FULL-61-13 sp001801865	76.1433	56	1408	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__2-02-FULL-61-13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 22:38:27,037] [INFO] GTDB search result was written to GCA_026710545.1_ASM2671054v1_genomic.fna/result_gtdb.tsv
[2023-06-26 22:38:27,038] [INFO] ===== GTDB Search completed =====
[2023-06-26 22:38:27,040] [INFO] DFAST_QC result json was written to GCA_026710545.1_ASM2671054v1_genomic.fna/dqc_result.json
[2023-06-26 22:38:27,041] [INFO] DFAST_QC completed!
[2023-06-26 22:38:27,041] [INFO] Total running time: 0h1m37s