[2024-01-24 13:32:41,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,395] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference
[2024-01-24 13:32:42,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,816] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e76b832-d16d-4c4f-a9e2-3c7a7598f227/GCF_002754935.1_ASM275493v1_genomic.fna.gz | prodigal -d GCF_002754935.1_ASM275493v1_genomic.fna/cds.fna -a GCF_002754935.1_ASM275493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:50,422] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:50,423] [INFO] Task started: HMMsearch
[2024-01-24 13:32:50,423] [INFO] Running command: hmmsearch --tblout GCF_002754935.1_ASM275493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference/reference_markers.hmm GCF_002754935.1_ASM275493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:50,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:50,658] [INFO] Found 6/6 markers.
[2024-01-24 13:32:50,687] [INFO] Query marker FASTA was written to GCF_002754935.1_ASM275493v1_genomic.fna/markers.fasta
[2024-01-24 13:32:50,688] [INFO] Task started: Blastn
[2024-01-24 13:32:50,688] [INFO] Running command: blastn -query GCF_002754935.1_ASM275493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference/reference_markers.fasta -out GCF_002754935.1_ASM275493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:51,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:51,317] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:51,317] [INFO] Target genome list was writen to GCF_002754935.1_ASM275493v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:51,328] [INFO] Task started: fastANI
[2024-01-24 13:32:51,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e76b832-d16d-4c4f-a9e2-3c7a7598f227/GCF_002754935.1_ASM275493v1_genomic.fna.gz --refList GCF_002754935.1_ASM275493v1_genomic.fna/target_genomes.txt --output GCF_002754935.1_ASM275493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:03,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:03,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:03,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:03,877] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:03,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:03,877] [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
Thermostichus lividus	strain=PCC 6715	GCA_002754935.1	33070	33070	type	True	100.0	886	886	95	conclusive
Thermosynechococcus vestitus	strain=BP-1	GCA_000011345.1	146786	146786	type	True	78.0155	326	886	95	below_threshold
Neosynechococcus sphagnicola	strain=CAUP A 1101	GCA_000775285.1	1501145	1501145	type	True	75.7432	53	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:03,879] [INFO] DFAST Taxonomy check result was written to GCF_002754935.1_ASM275493v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:03,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:03,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:03,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference/checkm_data
[2024-01-24 13:33:03,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:03,908] [INFO] Task started: CheckM
[2024-01-24 13:33:03,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002754935.1_ASM275493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002754935.1_ASM275493v1_genomic.fna/checkm_input GCF_002754935.1_ASM275493v1_genomic.fna/checkm_result
[2024-01-24 13:33:34,386] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:34,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:34,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:34,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:34,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002754935.1_ASM275493v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:34,410] [INFO] Task started: Blastn
[2024-01-24 13:33:34,410] [INFO] Running command: blastn -query GCF_002754935.1_ASM275493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbf5d26a-d3ca-4275-a3c0-3e30b63903eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002754935.1_ASM275493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:35,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:35,500] [INFO] Selected 20 target genomes.
[2024-01-24 13:33:35,500] [INFO] Target genome list was writen to GCF_002754935.1_ASM275493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:35,539] [INFO] Task started: fastANI
[2024-01-24 13:33:35,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e76b832-d16d-4c4f-a9e2-3c7a7598f227/GCF_002754935.1_ASM275493v1_genomic.fna.gz --refList GCF_002754935.1_ASM275493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002754935.1_ASM275493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:51,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:51,271] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:51,271] [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_002754935.1	s__Synechococcus_A lividus	100.0	886	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Synechococcus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008386235.1	s__Thermosynechococcus sp008386235	78.1985	378	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	97.03	97.03	0.96	0.96	2	-
GCF_003555505.1	s__Thermosynechococcus elongatus_B	78.137	383	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000505665.1	s__Thermosynechococcus sp000505665	78.075	313	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	99.74	99.69	1.00	0.99	4	-
GCA_015295825.1	s__Thermosynechococcus sp015295825	78.0684	348	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	99.88	99.88	0.93	0.93	2	-
GCF_000011345.1	s__Thermosynechococcus elongatus_A	78.0261	325	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	98.98	98.98	0.97	0.97	2	-
GCA_015296025.1	s__Thermosynechococcus sp015296025	77.9963	275	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316685.1	s__PCC-6312 sp000316685	76.2928	64	886	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__PCC-6312	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:51,273] [INFO] GTDB search result was written to GCF_002754935.1_ASM275493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:51,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:51,338] [INFO] DFAST_QC result json was written to GCF_002754935.1_ASM275493v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:51,338] [INFO] DFAST_QC completed!
[2024-01-24 13:33:51,338] [INFO] Total running time: 0h1m10s