[2023-03-16 10:35:15,179] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:15,179] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:15,179] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference
[2023-03-16 10:35:16,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:16,277] [INFO] Task started: Prodigal
[2023-03-16 10:35:16,277] [INFO] Running command: cat /var/lib/cwl/stg250b98c9-60df-47f1-8466-1719f9bdedfd/OceanDNA-b37725.fa | prodigal -d OceanDNA-b37725/cds.fna -a OceanDNA-b37725/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:31,123] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:31,123] [INFO] Task started: HMMsearch
[2023-03-16 10:35:31,124] [INFO] Running command: hmmsearch --tblout OceanDNA-b37725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference/reference_markers.hmm OceanDNA-b37725/protein.faa > /dev/null
[2023-03-16 10:35:31,304] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:31,305] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg250b98c9-60df-47f1-8466-1719f9bdedfd/OceanDNA-b37725.fa]
[2023-03-16 10:35:31,322] [INFO] Query marker FASTA was written to OceanDNA-b37725/markers.fasta
[2023-03-16 10:35:31,323] [INFO] Task started: Blastn
[2023-03-16 10:35:31,323] [INFO] Running command: blastn -query OceanDNA-b37725/markers.fasta -db /var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference/reference_markers.fasta -out OceanDNA-b37725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:31,906] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:31,907] [INFO] Selected 26 target genomes.
[2023-03-16 10:35:31,907] [INFO] Target genome list was writen to OceanDNA-b37725/target_genomes.txt
[2023-03-16 10:35:31,919] [INFO] Task started: fastANI
[2023-03-16 10:35:31,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg250b98c9-60df-47f1-8466-1719f9bdedfd/OceanDNA-b37725.fa --refList OceanDNA-b37725/target_genomes.txt --output OceanDNA-b37725/fastani_result.tsv --threads 1
[2023-03-16 10:35:46,078] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:46,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:46,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:46,082] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:46,082] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:35:46,082] [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
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.4214	56	794	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.0994	60	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:35:46,083] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37725/tc_result.tsv
[2023-03-16 10:35:46,083] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:46,083] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:46,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference/checkm_data
[2023-03-16 10:35:46,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:46,092] [INFO] Task started: CheckM
[2023-03-16 10:35:46,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37725/checkm_input OceanDNA-b37725/checkm_result
[2023-03-16 10:36:41,013] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:41,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:41,016] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:41,016] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:41,016] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37725/markers.fasta)
[2023-03-16 10:36:41,017] [INFO] Task started: Blastn
[2023-03-16 10:36:41,017] [INFO] Running command: blastn -query OceanDNA-b37725/markers.fasta -db /var/lib/cwl/stgf2710a46-cbe3-4857-8f62-2dd4d7616762/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:41,961] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:41,962] [INFO] Selected 10 target genomes.
[2023-03-16 10:36:41,962] [INFO] Target genome list was writen to OceanDNA-b37725/target_genomes_gtdb.txt
[2023-03-16 10:36:41,966] [INFO] Task started: fastANI
[2023-03-16 10:36:41,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg250b98c9-60df-47f1-8466-1719f9bdedfd/OceanDNA-b37725.fa --refList OceanDNA-b37725/target_genomes_gtdb.txt --output OceanDNA-b37725/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:36:46,283] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:46,289] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:36:46,290] [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_016778085.1	s__Luminiphilus sp016778085	98.64	438	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018222695.1	s__Luminiphilus sp018222695	93.6711	427	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331685.1	s__Luminiphilus sp003331685	90.7856	338	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520195.1	s__Luminiphilus sp902520195	84.9938	410	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_902518075.1	s__Luminiphilus sp902518075	84.8457	298	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623175.1	s__Luminiphilus sp902623175	84.735	521	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911345.1	s__Luminiphilus sp013911345	83.3252	203	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705465.1	s__Luminiphilus sp002705465	79.0338	103	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377985.1	s__Luminiphilus sp002377985	78.1596	168	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081075.1	s__Luminiphilus sp008081075	77.5185	94	794	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:36:46,290] [INFO] GTDB search result was written to OceanDNA-b37725/result_gtdb.tsv
[2023-03-16 10:36:46,291] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:36:46,292] [INFO] DFAST_QC result json was written to OceanDNA-b37725/dqc_result.json
[2023-03-16 10:36:46,292] [INFO] DFAST_QC completed!
[2023-03-16 10:36:46,292] [INFO] Total running time: 0h1m31s