[2023-06-07 18:14:56,643] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:14:56,647] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:14:56,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference
[2023-06-07 18:14:57,976] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:14:57,977] [INFO] Task started: Prodigal
[2023-06-07 18:14:57,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f3f62ed-326f-41ad-8acf-8947f232b09a/GCA_902614715.1_AG-919-C08_genomic.fna.gz | prodigal -d GCA_902614715.1_AG-919-C08_genomic.fna/cds.fna -a GCA_902614715.1_AG-919-C08_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:15:00,221] [INFO] Task succeeded: Prodigal
[2023-06-07 18:15:00,221] [INFO] Task started: HMMsearch
[2023-06-07 18:15:00,222] [INFO] Running command: hmmsearch --tblout GCA_902614715.1_AG-919-C08_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference/reference_markers.hmm GCA_902614715.1_AG-919-C08_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:15:00,459] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:15:00,460] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4f3f62ed-326f-41ad-8acf-8947f232b09a/GCA_902614715.1_AG-919-C08_genomic.fna.gz]
[2023-06-07 18:15:00,476] [INFO] Query marker FASTA was written to GCA_902614715.1_AG-919-C08_genomic.fna/markers.fasta
[2023-06-07 18:15:00,477] [INFO] Task started: Blastn
[2023-06-07 18:15:00,477] [INFO] Running command: blastn -query GCA_902614715.1_AG-919-C08_genomic.fna/markers.fasta -db /var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference/reference_markers.fasta -out GCA_902614715.1_AG-919-C08_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:00,975] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:00,978] [INFO] Selected 12 target genomes.
[2023-06-07 18:15:00,979] [INFO] Target genome list was writen to GCA_902614715.1_AG-919-C08_genomic.fna/target_genomes.txt
[2023-06-07 18:15:01,036] [INFO] Task started: fastANI
[2023-06-07 18:15:01,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3f62ed-326f-41ad-8acf-8947f232b09a/GCA_902614715.1_AG-919-C08_genomic.fna.gz --refList GCA_902614715.1_AG-919-C08_genomic.fna/target_genomes.txt --output GCA_902614715.1_AG-919-C08_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:15:06,681] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:06,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:15:06,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:15:06,684] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:15:06,684] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 18:15:06,684] [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
--------------------------------------------------------------------------------
[2023-06-07 18:15:06,686] [INFO] DFAST Taxonomy check result was written to GCA_902614715.1_AG-919-C08_genomic.fna/tc_result.tsv
[2023-06-07 18:15:06,687] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:15:06,687] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:15:06,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference/checkm_data
[2023-06-07 18:15:06,690] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:15:06,701] [INFO] Task started: CheckM
[2023-06-07 18:15:06,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902614715.1_AG-919-C08_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902614715.1_AG-919-C08_genomic.fna/checkm_input GCA_902614715.1_AG-919-C08_genomic.fna/checkm_result
[2023-06-07 18:15:22,063] [INFO] Task succeeded: CheckM
[2023-06-07 18:15:22,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:15:22,090] [INFO] ===== Completeness check finished =====
[2023-06-07 18:15:22,090] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:15:22,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902614715.1_AG-919-C08_genomic.fna/markers.fasta)
[2023-06-07 18:15:22,091] [INFO] Task started: Blastn
[2023-06-07 18:15:22,091] [INFO] Running command: blastn -query GCA_902614715.1_AG-919-C08_genomic.fna/markers.fasta -db /var/lib/cwl/stg78b22ee5-6d06-4059-b5ea-a2712aac4867/dqc_reference/reference_markers_gtdb.fasta -out GCA_902614715.1_AG-919-C08_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:22,639] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:22,642] [INFO] Selected 14 target genomes.
[2023-06-07 18:15:22,642] [INFO] Target genome list was writen to GCA_902614715.1_AG-919-C08_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:15:22,652] [INFO] Task started: fastANI
[2023-06-07 18:15:22,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f3f62ed-326f-41ad-8acf-8947f232b09a/GCA_902614715.1_AG-919-C08_genomic.fna.gz --refList GCA_902614715.1_AG-919-C08_genomic.fna/target_genomes_gtdb.txt --output GCA_902614715.1_AG-919-C08_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:15:26,086] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:26,099] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 18:15:26,099] [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_902617605.1	s__Prochlorococcus_A sp902617605	98.4173	172	246	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	conclusive
GCA_003210155.1	s__Prochlorococcus_A sp003210155	94.0834	206	246	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_003280655.1	s__Prochlorococcus_A sp003280655	93.9583	219	246	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.89	97.33	0.89	0.82	6	-
GCA_003281525.1	s__Prochlorococcus_A sp003281525	93.8459	202	246	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_902536775.1	s__Prochlorococcus_A sp902536775	93.6235	153	246	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_902538225.1	s__Prochlorococcus_A sp902538225	93.5765	140	246	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_003216915.1	s__Prochlorococcus_A sp003216915	93.5701	200	246	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_000635535.1	s__Prochlorococcus_A sp000635535	93.4728	96	246	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_003281285.1	s__Prochlorococcus_A sp003281285	93.4038	119	246	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_902616385.1	s__Prochlorococcus_A sp902616385	93.1144	204	246	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	92.8353	154	246	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_902606505.1	s__Prochlorococcus_A sp902606505	92.7618	181	246	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_003279055.1	s__Prochlorococcus_A sp003279055	92.3847	227	246	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_003214815.1	s__Prochlorococcus_A sp003214815	92.0546	228	246	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	-
--------------------------------------------------------------------------------
[2023-06-07 18:15:26,101] [INFO] GTDB search result was written to GCA_902614715.1_AG-919-C08_genomic.fna/result_gtdb.tsv
[2023-06-07 18:15:26,101] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:15:26,104] [INFO] DFAST_QC result json was written to GCA_902614715.1_AG-919-C08_genomic.fna/dqc_result.json
[2023-06-07 18:15:26,105] [INFO] DFAST_QC completed!
[2023-06-07 18:15:26,105] [INFO] Total running time: 0h0m29s