[2023-03-16 23:05:03,439] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference
[2023-03-16 23:05:04,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:04,690] [INFO] Task started: Prodigal
[2023-03-16 23:05:04,690] [INFO] Running command: cat /var/lib/cwl/stgf481c1c6-89f7-400f-a776-84f9a4e8e9c7/OceanDNA-b27479.fa | prodigal -d OceanDNA-b27479/cds.fna -a OceanDNA-b27479/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:10,632] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:10,633] [INFO] Task started: HMMsearch
[2023-03-16 23:05:10,633] [INFO] Running command: hmmsearch --tblout OceanDNA-b27479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference/reference_markers.hmm OceanDNA-b27479/protein.faa > /dev/null
[2023-03-16 23:05:10,793] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:10,794] [INFO] Found 6/6 markers.
[2023-03-16 23:05:10,803] [INFO] Query marker FASTA was written to OceanDNA-b27479/markers.fasta
[2023-03-16 23:05:10,803] [INFO] Task started: Blastn
[2023-03-16 23:05:10,803] [INFO] Running command: blastn -query OceanDNA-b27479/markers.fasta -db /var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference/reference_markers.fasta -out OceanDNA-b27479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:11,697] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:11,698] [INFO] Selected 12 target genomes.
[2023-03-16 23:05:11,698] [INFO] Target genome list was writen to OceanDNA-b27479/target_genomes.txt
[2023-03-16 23:05:11,706] [INFO] Task started: fastANI
[2023-03-16 23:05:11,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgf481c1c6-89f7-400f-a776-84f9a4e8e9c7/OceanDNA-b27479.fa --refList OceanDNA-b27479/target_genomes.txt --output OceanDNA-b27479/fastani_result.tsv --threads 1
[2023-03-16 23:05:17,267] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:17,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:17,268] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:17,268] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:17,268] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:05:17,268] [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
--------------------------------------------------------------------------------
[2023-03-16 23:05:17,268] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27479/tc_result.tsv
[2023-03-16 23:05:17,268] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:17,268] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:17,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference/checkm_data
[2023-03-16 23:05:17,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:17,280] [INFO] Task started: CheckM
[2023-03-16 23:05:17,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27479/checkm_input OceanDNA-b27479/checkm_result
[2023-03-16 23:05:42,558] [INFO] Task succeeded: CheckM
[2023-03-16 23:05:42,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:05:42,560] [INFO] ===== Completeness check finished =====
[2023-03-16 23:05:42,561] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:05:42,561] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27479/markers.fasta)
[2023-03-16 23:05:42,562] [INFO] Task started: Blastn
[2023-03-16 23:05:42,562] [INFO] Running command: blastn -query OceanDNA-b27479/markers.fasta -db /var/lib/cwl/stg8380f6b8-66b8-46c9-bf42-060d2d84e4f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:44,294] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:44,295] [INFO] Selected 10 target genomes.
[2023-03-16 23:05:44,295] [INFO] Target genome list was writen to OceanDNA-b27479/target_genomes_gtdb.txt
[2023-03-16 23:05:44,668] [INFO] Task started: fastANI
[2023-03-16 23:05:44,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgf481c1c6-89f7-400f-a776-84f9a4e8e9c7/OceanDNA-b27479.fa --refList OceanDNA-b27479/target_genomes_gtdb.txt --output OceanDNA-b27479/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:05:46,920] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:46,926] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:05:46,926] [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_002699615.1	s__TMED25 sp002699615	98.0107	328	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	97.16	95.98	0.85	0.81	4	conclusive
GCA_902633855.1	s__TMED25 sp902633855	83.723	255	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.57	99.57	0.84	0.84	2	-
GCA_902613795.1	s__TMED25 sp902613795	83.3709	300	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.47	99.34	0.93	0.93	3	-
GCA_902538185.1	s__TMED25 sp902538185	83.2889	194	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694595.1	s__TMED25 sp002694595	82.5473	116	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.56	98.18	0.76	0.67	3	-
GCA_902632055.1	s__TMED25 sp902632055	82.5094	221	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002168075.1	s__TMED25 sp002168075	77.335	75	369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.97	97.02	0.94	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-16 23:05:46,926] [INFO] GTDB search result was written to OceanDNA-b27479/result_gtdb.tsv
[2023-03-16 23:05:46,926] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:05:46,927] [INFO] DFAST_QC result json was written to OceanDNA-b27479/dqc_result.json
[2023-03-16 23:05:46,927] [INFO] DFAST_QC completed!
[2023-03-16 23:05:46,927] [INFO] Total running time: 0h0m43s