[2023-06-16 19:10:59,553] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:10:59,554] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:10:59,554] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference
[2023-06-16 19:11:00,708] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:11:00,708] [INFO] Task started: Prodigal
[2023-06-16 19:11:00,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg88071c6f-d3c7-49f5-a6d6-b00473d9284a/GCA_009846095.1_ASM984609v1_genomic.fna.gz | prodigal -d GCA_009846095.1_ASM984609v1_genomic.fna/cds.fna -a GCA_009846095.1_ASM984609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:11:11,844] [INFO] Task succeeded: Prodigal
[2023-06-16 19:11:11,845] [INFO] Task started: HMMsearch
[2023-06-16 19:11:11,845] [INFO] Running command: hmmsearch --tblout GCA_009846095.1_ASM984609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference/reference_markers.hmm GCA_009846095.1_ASM984609v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:11:12,045] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:11:12,046] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88071c6f-d3c7-49f5-a6d6-b00473d9284a/GCA_009846095.1_ASM984609v1_genomic.fna.gz]
[2023-06-16 19:11:12,066] [INFO] Query marker FASTA was written to GCA_009846095.1_ASM984609v1_genomic.fna/markers.fasta
[2023-06-16 19:11:12,067] [INFO] Task started: Blastn
[2023-06-16 19:11:12,067] [INFO] Running command: blastn -query GCA_009846095.1_ASM984609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference/reference_markers.fasta -out GCA_009846095.1_ASM984609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:12,626] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:12,630] [INFO] Selected 26 target genomes.
[2023-06-16 19:11:12,630] [INFO] Target genome list was writen to GCA_009846095.1_ASM984609v1_genomic.fna/target_genomes.txt
[2023-06-16 19:11:12,631] [INFO] Task started: fastANI
[2023-06-16 19:11:12,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg88071c6f-d3c7-49f5-a6d6-b00473d9284a/GCA_009846095.1_ASM984609v1_genomic.fna.gz --refList GCA_009846095.1_ASM984609v1_genomic.fna/target_genomes.txt --output GCA_009846095.1_ASM984609v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:11:29,114] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:29,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:11:29,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:11:29,117] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:11:29,117] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:11:29,117] [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
--------------------------------------------------------------------------------
[2023-06-16 19:11:29,119] [INFO] DFAST Taxonomy check result was written to GCA_009846095.1_ASM984609v1_genomic.fna/tc_result.tsv
[2023-06-16 19:11:29,120] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:11:29,120] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:11:29,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference/checkm_data
[2023-06-16 19:11:29,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:11:29,146] [INFO] Task started: CheckM
[2023-06-16 19:11:29,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009846095.1_ASM984609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009846095.1_ASM984609v1_genomic.fna/checkm_input GCA_009846095.1_ASM984609v1_genomic.fna/checkm_result
[2023-06-16 19:12:03,469] [INFO] Task succeeded: CheckM
[2023-06-16 19:12:03,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 19:12:03,488] [INFO] ===== Completeness check finished =====
[2023-06-16 19:12:03,488] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:12:03,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009846095.1_ASM984609v1_genomic.fna/markers.fasta)
[2023-06-16 19:12:03,490] [INFO] Task started: Blastn
[2023-06-16 19:12:03,490] [INFO] Running command: blastn -query GCA_009846095.1_ASM984609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdad8fa2-6a50-4297-978e-7a1a7971bb5c/dqc_reference/reference_markers_gtdb.fasta -out GCA_009846095.1_ASM984609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:12:04,262] [INFO] Task succeeded: Blastn
[2023-06-16 19:12:04,265] [INFO] Selected 7 target genomes.
[2023-06-16 19:12:04,265] [INFO] Target genome list was writen to GCA_009846095.1_ASM984609v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:12:04,266] [INFO] Task started: fastANI
[2023-06-16 19:12:04,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg88071c6f-d3c7-49f5-a6d6-b00473d9284a/GCA_009846095.1_ASM984609v1_genomic.fna.gz --refList GCA_009846095.1_ASM984609v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009846095.1_ASM984609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:12:07,061] [INFO] Task succeeded: fastANI
[2023-06-16 19:12:07,067] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:12:07,067] [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_009836025.1	s__Synechococcus_B sp009836025	98.7373	480	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	98.45	97.12	0.89	0.82	12	conclusive
GCF_000586015.1	s__Synechococcus_B spongiarum_F	89.4726	309	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	98.37	98.37	0.72	0.72	2	-
GCA_009840445.1	s__Synechococcus_B sp009840445	86.4915	433	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	99.43	99.30	0.96	0.94	7	-
GCA_001007665.1	s__Synechococcus_B spongiarum_B	86.0008	423	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900047545.1	s__Synechococcus_B spongiarum_C	85.5287	290	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002018045.1	s__Synechococcus_B spongiarum_E	85.4454	334	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	98.89	98.75	0.82	0.77	4	-
GCA_007571085.1	s__Synechococcus_B sp007571085	78.889	224	540	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_B	95.0	99.41	99.41	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:12:07,069] [INFO] GTDB search result was written to GCA_009846095.1_ASM984609v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:12:07,070] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:12:07,072] [INFO] DFAST_QC result json was written to GCA_009846095.1_ASM984609v1_genomic.fna/dqc_result.json
[2023-06-16 19:12:07,072] [INFO] DFAST_QC completed!
[2023-06-16 19:12:07,072] [INFO] Total running time: 0h1m8s