[2023-03-18 22:44:57,814] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,814] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference
[2023-03-18 22:44:58,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:58,938] [INFO] Task started: Prodigal
[2023-03-18 22:44:58,938] [INFO] Running command: cat /var/lib/cwl/stg29adfc73-3162-46fc-8331-ef597ad1b427/OceanDNA-b16363.fa | prodigal -d OceanDNA-b16363/cds.fna -a OceanDNA-b16363/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:06,843] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:06,843] [INFO] Task started: HMMsearch
[2023-03-18 22:45:06,843] [INFO] Running command: hmmsearch --tblout OceanDNA-b16363/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference/reference_markers.hmm OceanDNA-b16363/protein.faa > /dev/null
[2023-03-18 22:45:07,017] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:07,017] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg29adfc73-3162-46fc-8331-ef597ad1b427/OceanDNA-b16363.fa]
[2023-03-18 22:45:07,028] [INFO] Query marker FASTA was written to OceanDNA-b16363/markers.fasta
[2023-03-18 22:45:07,029] [INFO] Task started: Blastn
[2023-03-18 22:45:07,029] [INFO] Running command: blastn -query OceanDNA-b16363/markers.fasta -db /var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference/reference_markers.fasta -out OceanDNA-b16363/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:07,572] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:07,573] [INFO] Selected 9 target genomes.
[2023-03-18 22:45:07,573] [INFO] Target genome list was writen to OceanDNA-b16363/target_genomes.txt
[2023-03-18 22:45:07,579] [INFO] Task started: fastANI
[2023-03-18 22:45:07,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg29adfc73-3162-46fc-8331-ef597ad1b427/OceanDNA-b16363.fa --refList OceanDNA-b16363/target_genomes.txt --output OceanDNA-b16363/fastani_result.tsv --threads 1
[2023-03-18 22:45:10,605] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:10,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:10,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:10,606] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:10,606] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:45:10,606] [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
--------------------------------------------------------------------------------
[2023-03-18 22:45:10,606] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16363/tc_result.tsv
[2023-03-18 22:45:10,606] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:10,607] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:10,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference/checkm_data
[2023-03-18 22:45:10,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:10,612] [INFO] Task started: CheckM
[2023-03-18 22:45:10,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16363/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16363/checkm_input OceanDNA-b16363/checkm_result
[2023-03-18 22:45:35,577] [INFO] Task succeeded: CheckM
[2023-03-18 22:45:35,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:45:35,579] [INFO] ===== Completeness check finished =====
[2023-03-18 22:45:35,579] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:45:35,580] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16363/markers.fasta)
[2023-03-18 22:45:35,580] [INFO] Task started: Blastn
[2023-03-18 22:45:35,580] [INFO] Running command: blastn -query OceanDNA-b16363/markers.fasta -db /var/lib/cwl/stg31cf20e1-cc8d-4073-9c24-7f5164c0c314/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16363/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:36,480] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:36,481] [INFO] Selected 11 target genomes.
[2023-03-18 22:45:36,481] [INFO] Target genome list was writen to OceanDNA-b16363/target_genomes_gtdb.txt
[2023-03-18 22:45:36,493] [INFO] Task started: fastANI
[2023-03-18 22:45:36,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg29adfc73-3162-46fc-8331-ef597ad1b427/OceanDNA-b16363.fa --refList OceanDNA-b16363/target_genomes_gtdb.txt --output OceanDNA-b16363/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:45:40,167] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:40,174] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 22:45:40,174] [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_000012465.1	s__Prochlorococcus_B marinus_B	97.6823	409	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	96.72	95.73	0.94	0.90	18	inconclusive
GCA_003279635.1	s__Prochlorococcus_B sp003279635	95.3253	354	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	95.70	95.70	0.77	0.77	2	inconclusive
GCA_003213355.1	s__Prochlorococcus_B sp003213355	94.1903	269	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757865.1	s__Prochlorococcus_B sp000757865	94.1547	404	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284375.1	s__Prochlorococcus_B sp003284375	92.4255	290	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284445.1	s__Prochlorococcus_B sp003284445	92.0347	297	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216175.1	s__Prochlorococcus_B sp003216175	89.7511	335	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209755.1	s__Prochlorococcus_B sp003209755	89.6469	360	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216595.1	s__Prochlorococcus_B sp003216595	89.5772	341	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216955.1	s__Prochlorococcus_B sp003216955	88.9254	360	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216575.1	s__Prochlorococcus_B sp003216575	86.5099	312	410	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:45:40,174] [INFO] GTDB search result was written to OceanDNA-b16363/result_gtdb.tsv
[2023-03-18 22:45:40,174] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:45:40,175] [INFO] DFAST_QC result json was written to OceanDNA-b16363/dqc_result.json
[2023-03-18 22:45:40,175] [INFO] DFAST_QC completed!
[2023-03-18 22:45:40,175] [INFO] Total running time: 0h0m42s