[2024-01-24 12:40:50,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference
[2024-01-24 12:40:51,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,443] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a6b3468-e04e-4d90-ada0-d505e73f4e31/GCF_000484535.1_ASM48453v1_genomic.fna.gz | prodigal -d GCF_000484535.1_ASM48453v1_genomic.fna/cds.fna -a GCF_000484535.1_ASM48453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:04,607] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:04,607] [INFO] Task started: HMMsearch
[2024-01-24 12:41:04,607] [INFO] Running command: hmmsearch --tblout GCF_000484535.1_ASM48453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference/reference_markers.hmm GCF_000484535.1_ASM48453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:04,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:04,908] [INFO] Found 6/6 markers.
[2024-01-24 12:41:04,957] [INFO] Query marker FASTA was written to GCF_000484535.1_ASM48453v1_genomic.fna/markers.fasta
[2024-01-24 12:41:04,957] [INFO] Task started: Blastn
[2024-01-24 12:41:04,958] [INFO] Running command: blastn -query GCF_000484535.1_ASM48453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference/reference_markers.fasta -out GCF_000484535.1_ASM48453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:05,558] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:05,563] [INFO] Selected 12 target genomes.
[2024-01-24 12:41:05,563] [INFO] Target genome list was writen to GCF_000484535.1_ASM48453v1_genomic.fna/target_genomes.txt
[2024-01-24 12:41:05,569] [INFO] Task started: fastANI
[2024-01-24 12:41:05,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a6b3468-e04e-4d90-ada0-d505e73f4e31/GCF_000484535.1_ASM48453v1_genomic.fna.gz --refList GCF_000484535.1_ASM48453v1_genomic.fna/target_genomes.txt --output GCF_000484535.1_ASM48453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:15,054] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:15,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:15,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:15,064] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:41:15,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:15,065] [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
Gloeobacter kilaueensis	strain=JS1	GCA_000484535.1	1416614	1416614	type	True	100.0	1574	1574	95	conclusive
Gloeobacter violaceus	strain=PCC 7421	GCA_000011385.1	33072	33072	type	True	78.8928	635	1574	95	below_threshold
Gloeobacter morelensis		GCA_021018745.1	2907343	2907343	type	True	78.7494	643	1574	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	74.8886	52	1574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:15,066] [INFO] DFAST Taxonomy check result was written to GCF_000484535.1_ASM48453v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:15,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:15,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:15,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference/checkm_data
[2024-01-24 12:41:15,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:15,115] [INFO] Task started: CheckM
[2024-01-24 12:41:15,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000484535.1_ASM48453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000484535.1_ASM48453v1_genomic.fna/checkm_input GCF_000484535.1_ASM48453v1_genomic.fna/checkm_result
[2024-01-24 12:41:54,799] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:54,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:54,824] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:54,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:54,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000484535.1_ASM48453v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:54,826] [INFO] Task started: Blastn
[2024-01-24 12:41:54,826] [INFO] Running command: blastn -query GCF_000484535.1_ASM48453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb046bde2-a13b-4660-8fc9-8af8968a1f55/dqc_reference/reference_markers_gtdb.fasta -out GCF_000484535.1_ASM48453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:55,665] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:55,668] [INFO] Selected 17 target genomes.
[2024-01-24 12:41:55,669] [INFO] Target genome list was writen to GCF_000484535.1_ASM48453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:55,716] [INFO] Task started: fastANI
[2024-01-24 12:41:55,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a6b3468-e04e-4d90-ada0-d505e73f4e31/GCF_000484535.1_ASM48453v1_genomic.fna.gz --refList GCF_000484535.1_ASM48453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000484535.1_ASM48453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:07,871] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:07,886] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:07,886] [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_000484535.1	s__Gloeobacter kilaueensis	100.0	1574	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__Gloeobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000011385.1	s__Gloeobacter violaceus	78.908	632	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__Gloeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380935.1	s__JACMIX01 sp014380935	76.0796	118	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__JACMIX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003017855.1	s__Nodosilinea sp003017855	75.8994	69	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCA_003241845.1	s__Nodosilinea antarctica	75.8866	67	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	98.34	98.34	0.86	0.86	2	-
GCF_015840715.1	s__Cyanobium sp015840715	75.8727	61	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379585.1	s__JACMLN01 sp014379585	75.8453	79	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Gloeobacterales;f__Gloeobacteraceae;g__JACMLN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249105.1	s__Nodosilinea sp003249105	75.7711	68	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038415.1	s__Cyanobium sp019038415	75.6722	66	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252705.1	s__Vulcanococcus limneticus	75.5401	72	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907855.1	s__Cyanobium sp903907855	75.4495	56	1574	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	99.37	99.37	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:07,888] [INFO] GTDB search result was written to GCF_000484535.1_ASM48453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:07,888] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:07,891] [INFO] DFAST_QC result json was written to GCF_000484535.1_ASM48453v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:07,891] [INFO] DFAST_QC completed!
[2024-01-24 12:42:07,891] [INFO] Total running time: 0h1m18s