[2023-06-28 20:41:06,822] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:41:06,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:41:06,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference
[2023-06-28 20:41:08,139] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:41:08,140] [INFO] Task started: Prodigal
[2023-06-28 20:41:08,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg89acb258-8ae4-42eb-a871-9f6ed0eb5e1a/GCA_012033055.1_ASM1203305v1_genomic.fna.gz | prodigal -d GCA_012033055.1_ASM1203305v1_genomic.fna/cds.fna -a GCA_012033055.1_ASM1203305v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:41:17,463] [INFO] Task succeeded: Prodigal
[2023-06-28 20:41:17,464] [INFO] Task started: HMMsearch
[2023-06-28 20:41:17,464] [INFO] Running command: hmmsearch --tblout GCA_012033055.1_ASM1203305v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference/reference_markers.hmm GCA_012033055.1_ASM1203305v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:41:17,747] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:41:17,748] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg89acb258-8ae4-42eb-a871-9f6ed0eb5e1a/GCA_012033055.1_ASM1203305v1_genomic.fna.gz]
[2023-06-28 20:41:17,795] [INFO] Query marker FASTA was written to GCA_012033055.1_ASM1203305v1_genomic.fna/markers.fasta
[2023-06-28 20:41:17,795] [INFO] Task started: Blastn
[2023-06-28 20:41:17,795] [INFO] Running command: blastn -query GCA_012033055.1_ASM1203305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference/reference_markers.fasta -out GCA_012033055.1_ASM1203305v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:18,425] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:18,430] [INFO] Selected 25 target genomes.
[2023-06-28 20:41:18,431] [INFO] Target genome list was writen to GCA_012033055.1_ASM1203305v1_genomic.fna/target_genomes.txt
[2023-06-28 20:41:18,434] [INFO] Task started: fastANI
[2023-06-28 20:41:18,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg89acb258-8ae4-42eb-a871-9f6ed0eb5e1a/GCA_012033055.1_ASM1203305v1_genomic.fna.gz --refList GCA_012033055.1_ASM1203305v1_genomic.fna/target_genomes.txt --output GCA_012033055.1_ASM1203305v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:41:35,148] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:35,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:41:35,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:41:35,151] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:41:35,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 20:41:35,152] [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 20:41:35,155] [INFO] DFAST Taxonomy check result was written to GCA_012033055.1_ASM1203305v1_genomic.fna/tc_result.tsv
[2023-06-28 20:41:35,156] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:41:35,156] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:41:35,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference/checkm_data
[2023-06-28 20:41:35,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:41:35,206] [INFO] Task started: CheckM
[2023-06-28 20:41:35,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012033055.1_ASM1203305v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012033055.1_ASM1203305v1_genomic.fna/checkm_input GCA_012033055.1_ASM1203305v1_genomic.fna/checkm_result
[2023-06-28 20:42:07,711] [INFO] Task succeeded: CheckM
[2023-06-28 20:42:07,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:42:07,738] [INFO] ===== Completeness check finished =====
[2023-06-28 20:42:07,738] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:42:07,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012033055.1_ASM1203305v1_genomic.fna/markers.fasta)
[2023-06-28 20:42:07,739] [INFO] Task started: Blastn
[2023-06-28 20:42:07,739] [INFO] Running command: blastn -query GCA_012033055.1_ASM1203305v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13c5a424-a11e-4e5b-84ae-010094880f8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_012033055.1_ASM1203305v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:42:08,681] [INFO] Task succeeded: Blastn
[2023-06-28 20:42:08,686] [INFO] Selected 18 target genomes.
[2023-06-28 20:42:08,686] [INFO] Target genome list was writen to GCA_012033055.1_ASM1203305v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:42:08,696] [INFO] Task started: fastANI
[2023-06-28 20:42:08,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg89acb258-8ae4-42eb-a871-9f6ed0eb5e1a/GCA_012033055.1_ASM1203305v1_genomic.fna.gz --refList GCA_012033055.1_ASM1203305v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012033055.1_ASM1203305v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:42:22,728] [INFO] Task succeeded: fastANI
[2023-06-28 20:42:22,738] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:42:22,739] [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_012033055.1	s__Limnothrix sp012033055	100.0	1274	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001904615.1	s__Limnothrix rosea	77.9067	461	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316605.1	s__Limnothrix sp000316605	77.6228	405	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693275.1	s__Limnothrix sp001693275	77.0412	314	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	96.93	96.67	0.92	0.91	11	-
GCF_002356215.1	s__Limnothrix sp002356215	76.9729	253	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	98.53	98.53	0.95	0.95	2	-
GCF_001693255.1	s__Limnothrix sp001693255	76.955	289	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Cyanobacteriaceae;g__Limnothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693875.1	s__Spirulina sp007693875	75.6289	53	1284	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Spirulinaceae;g__Spirulina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:42:22,741] [INFO] GTDB search result was written to GCA_012033055.1_ASM1203305v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:42:22,741] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:42:22,744] [INFO] DFAST_QC result json was written to GCA_012033055.1_ASM1203305v1_genomic.fna/dqc_result.json
[2023-06-28 20:42:22,744] [INFO] DFAST_QC completed!
[2023-06-28 20:42:22,744] [INFO] Total running time: 0h1m16s