[2023-06-08 20:04:30,637] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:04:30,650] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:04:30,650] [INFO] DQC Reference Directory: /var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference
[2023-06-08 20:04:33,035] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:04:33,037] [INFO] Task started: Prodigal
[2023-06-08 20:04:33,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg34814478-534b-49d5-a4ea-e6a7db5d513d/GCA_902615475.1_AG-891-O18_genomic.fna.gz | prodigal -d GCA_902615475.1_AG-891-O18_genomic.fna/cds.fna -a GCA_902615475.1_AG-891-O18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:04:35,098] [INFO] Task succeeded: Prodigal
[2023-06-08 20:04:35,098] [INFO] Task started: HMMsearch
[2023-06-08 20:04:35,098] [INFO] Running command: hmmsearch --tblout GCA_902615475.1_AG-891-O18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference/reference_markers.hmm GCA_902615475.1_AG-891-O18_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:04:35,281] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:04:35,283] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg34814478-534b-49d5-a4ea-e6a7db5d513d/GCA_902615475.1_AG-891-O18_genomic.fna.gz]
[2023-06-08 20:04:35,302] [INFO] Query marker FASTA was written to GCA_902615475.1_AG-891-O18_genomic.fna/markers.fasta
[2023-06-08 20:04:35,302] [INFO] Task started: Blastn
[2023-06-08 20:04:35,302] [INFO] Running command: blastn -query GCA_902615475.1_AG-891-O18_genomic.fna/markers.fasta -db /var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference/reference_markers.fasta -out GCA_902615475.1_AG-891-O18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:36,899] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:36,903] [INFO] Selected 6 target genomes.
[2023-06-08 20:04:36,903] [INFO] Target genome list was writen to GCA_902615475.1_AG-891-O18_genomic.fna/target_genomes.txt
[2023-06-08 20:04:36,907] [INFO] Task started: fastANI
[2023-06-08 20:04:36,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg34814478-534b-49d5-a4ea-e6a7db5d513d/GCA_902615475.1_AG-891-O18_genomic.fna.gz --refList GCA_902615475.1_AG-891-O18_genomic.fna/target_genomes.txt --output GCA_902615475.1_AG-891-O18_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:04:40,001] [INFO] Task succeeded: fastANI
[2023-06-08 20:04:40,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:04:40,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:04:40,004] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:04:40,005] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 20:04:40,005] [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 20:04:40,008] [INFO] DFAST Taxonomy check result was written to GCA_902615475.1_AG-891-O18_genomic.fna/tc_result.tsv
[2023-06-08 20:04:40,008] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:04:40,009] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:04:40,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference/checkm_data
[2023-06-08 20:04:40,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:04:40,030] [INFO] Task started: CheckM
[2023-06-08 20:04:40,030] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902615475.1_AG-891-O18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902615475.1_AG-891-O18_genomic.fna/checkm_input GCA_902615475.1_AG-891-O18_genomic.fna/checkm_result
[2023-06-08 20:04:54,359] [INFO] Task succeeded: CheckM
[2023-06-08 20:04:54,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:04:54,378] [INFO] ===== Completeness check finished =====
[2023-06-08 20:04:54,378] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:04:54,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902615475.1_AG-891-O18_genomic.fna/markers.fasta)
[2023-06-08 20:04:54,379] [INFO] Task started: Blastn
[2023-06-08 20:04:54,379] [INFO] Running command: blastn -query GCA_902615475.1_AG-891-O18_genomic.fna/markers.fasta -db /var/lib/cwl/stgc386dfa6-44ed-4928-8871-e5024cd19286/dqc_reference/reference_markers_gtdb.fasta -out GCA_902615475.1_AG-891-O18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:04:54,943] [INFO] Task succeeded: Blastn
[2023-06-08 20:04:54,947] [INFO] Selected 10 target genomes.
[2023-06-08 20:04:54,947] [INFO] Target genome list was writen to GCA_902615475.1_AG-891-O18_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:04:54,953] [INFO] Task started: fastANI
[2023-06-08 20:04:54,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg34814478-534b-49d5-a4ea-e6a7db5d513d/GCA_902615475.1_AG-891-O18_genomic.fna.gz --refList GCA_902615475.1_AG-891-O18_genomic.fna/target_genomes_gtdb.txt --output GCA_902615475.1_AG-891-O18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:04:57,525] [INFO] Task succeeded: fastANI
[2023-06-08 20:04:57,540] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:04:57,540] [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
GCF_002025865.1	s__Prochlorococcus_A sp002025865	96.5101	150	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	96.75	96.29	0.67	0.64	5	conclusive
GCA_000635495.1	s__Prochlorococcus_A sp000635495	94.7855	203	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	98.33	95.15	0.88	0.77	73	-
GCA_003278545.1	s__Prochlorococcus_A sp003278545	94.5504	205	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002026005.1	s__Prochlorococcus_A sp002026005	94.291	152	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.72	95.72	0.86	0.86	2	-
GCA_003213375.1	s__Prochlorococcus_A sp003213375	94.2656	130	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	96.27	96.27	0.94	0.94	2	-
GCA_003216915.1	s__Prochlorococcus_A sp003216915	93.927	187	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003214315.1	s__Prochlorococcus_A sp003214315	93.1125	200	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211415.1	s__Prochlorococcus_A sp003211415	93.1031	130	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	95.46	95.46	0.66	0.66	2	-
GCA_902539115.1	s__Prochlorococcus_A sp902539115	92.9495	144	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001180305.1	s__Prochlorococcus_A marinus_K	90.023	162	230	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:04:57,543] [INFO] GTDB search result was written to GCA_902615475.1_AG-891-O18_genomic.fna/result_gtdb.tsv
[2023-06-08 20:04:57,544] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:04:57,547] [INFO] DFAST_QC result json was written to GCA_902615475.1_AG-891-O18_genomic.fna/dqc_result.json
[2023-06-08 20:04:57,547] [INFO] DFAST_QC completed!
[2023-06-08 20:04:57,548] [INFO] Total running time: 0h0m27s