[2023-03-18 10:05:40,208] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:05:40,208] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:05:40,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference
[2023-03-18 10:05:41,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:05:41,302] [INFO] Task started: Prodigal
[2023-03-18 10:05:41,302] [INFO] Running command: cat /var/lib/cwl/stgbab9962d-e585-44ab-a9a0-0b263f5a4140/OceanDNA-b40548.fa | prodigal -d OceanDNA-b40548/cds.fna -a OceanDNA-b40548/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:05:54,055] [INFO] Task succeeded: Prodigal
[2023-03-18 10:05:54,056] [INFO] Task started: HMMsearch
[2023-03-18 10:05:54,056] [INFO] Running command: hmmsearch --tblout OceanDNA-b40548/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference/reference_markers.hmm OceanDNA-b40548/protein.faa > /dev/null
[2023-03-18 10:05:54,234] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:05:54,235] [INFO] Found 6/6 markers.
[2023-03-18 10:05:54,251] [INFO] Query marker FASTA was written to OceanDNA-b40548/markers.fasta
[2023-03-18 10:05:54,252] [INFO] Task started: Blastn
[2023-03-18 10:05:54,252] [INFO] Running command: blastn -query OceanDNA-b40548/markers.fasta -db /var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference/reference_markers.fasta -out OceanDNA-b40548/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:05:54,774] [INFO] Task succeeded: Blastn
[2023-03-18 10:05:54,784] [INFO] Selected 29 target genomes.
[2023-03-18 10:05:54,784] [INFO] Target genome list was writen to OceanDNA-b40548/target_genomes.txt
[2023-03-18 10:05:54,803] [INFO] Task started: fastANI
[2023-03-18 10:05:54,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab9962d-e585-44ab-a9a0-0b263f5a4140/OceanDNA-b40548.fa --refList OceanDNA-b40548/target_genomes.txt --output OceanDNA-b40548/fastani_result.tsv --threads 1
[2023-03-18 10:06:11,313] [INFO] Task succeeded: fastANI
[2023-03-18 10:06:11,314] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:06:11,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:06:11,314] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:06:11,314] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:06:11,314] [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 10:06:11,314] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40548/tc_result.tsv
[2023-03-18 10:06:11,314] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:06:11,314] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:06:11,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference/checkm_data
[2023-03-18 10:06:11,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:06:11,325] [INFO] Task started: CheckM
[2023-03-18 10:06:11,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40548/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40548/checkm_input OceanDNA-b40548/checkm_result
[2023-03-18 10:06:47,045] [INFO] Task succeeded: CheckM
[2023-03-18 10:06:47,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:06:47,048] [INFO] ===== Completeness check finished =====
[2023-03-18 10:06:47,048] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:06:47,048] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40548/markers.fasta)
[2023-03-18 10:06:47,050] [INFO] Task started: Blastn
[2023-03-18 10:06:47,050] [INFO] Running command: blastn -query OceanDNA-b40548/markers.fasta -db /var/lib/cwl/stg289a6490-6643-4c48-a3a0-02c193829733/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40548/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:06:47,783] [INFO] Task succeeded: Blastn
[2023-03-18 10:06:47,784] [INFO] Selected 8 target genomes.
[2023-03-18 10:06:47,784] [INFO] Target genome list was writen to OceanDNA-b40548/target_genomes_gtdb.txt
[2023-03-18 10:06:47,794] [INFO] Task started: fastANI
[2023-03-18 10:06:47,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab9962d-e585-44ab-a9a0-0b263f5a4140/OceanDNA-b40548.fa --refList OceanDNA-b40548/target_genomes_gtdb.txt --output OceanDNA-b40548/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:06:52,189] [INFO] Task succeeded: fastANI
[2023-03-18 10:06:52,194] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 10:06:52,194] [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_008081045.1	s__UBA9145 sp008081045	98.1757	656	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.92	98.40	0.89	0.82	4	conclusive
GCA_902537815.1	s__UBA9145 sp902537815	94.4226	465	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597095.1	s__UBA9145 sp902597095	94.0701	502	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691885.1	s__UBA9145 sp002691885	87.0668	508	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002729315.1	s__UBA9145 sp002729315	86.2668	515	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719575.1	s__UBA9145 sp002719575	78.8096	313	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477465.1	s__UBA9145 sp002477465	76.5307	108	717	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
--------------------------------------------------------------------------------
[2023-03-18 10:06:52,197] [INFO] GTDB search result was written to OceanDNA-b40548/result_gtdb.tsv
[2023-03-18 10:06:52,200] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:06:52,203] [INFO] DFAST_QC result json was written to OceanDNA-b40548/dqc_result.json
[2023-03-18 10:06:52,203] [INFO] DFAST_QC completed!
[2023-03-18 10:06:52,203] [INFO] Total running time: 0h1m12s