[2023-03-16 06:03:26,021] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:26,021] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:26,021] [INFO] DQC Reference Directory: /var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference
[2023-03-16 06:03:27,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:27,116] [INFO] Task started: Prodigal
[2023-03-16 06:03:27,117] [INFO] Running command: cat /var/lib/cwl/stgbefabd7a-bcc1-40f1-a934-28209a7b4ffe/OceanDNA-b38100.fa | prodigal -d OceanDNA-b38100/cds.fna -a OceanDNA-b38100/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:40,895] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:40,895] [INFO] Task started: HMMsearch
[2023-03-16 06:03:40,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b38100/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference/reference_markers.hmm OceanDNA-b38100/protein.faa > /dev/null
[2023-03-16 06:03:41,068] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:41,069] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbefabd7a-bcc1-40f1-a934-28209a7b4ffe/OceanDNA-b38100.fa]
[2023-03-16 06:03:41,085] [INFO] Query marker FASTA was written to OceanDNA-b38100/markers.fasta
[2023-03-16 06:03:41,086] [INFO] Task started: Blastn
[2023-03-16 06:03:41,086] [INFO] Running command: blastn -query OceanDNA-b38100/markers.fasta -db /var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference/reference_markers.fasta -out OceanDNA-b38100/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:41,646] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:41,647] [INFO] Selected 23 target genomes.
[2023-03-16 06:03:41,647] [INFO] Target genome list was writen to OceanDNA-b38100/target_genomes.txt
[2023-03-16 06:03:41,661] [INFO] Task started: fastANI
[2023-03-16 06:03:41,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefabd7a-bcc1-40f1-a934-28209a7b4ffe/OceanDNA-b38100.fa --refList OceanDNA-b38100/target_genomes.txt --output OceanDNA-b38100/fastani_result.tsv --threads 1
[2023-03-16 06:03:56,124] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:56,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:03:56,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:03:56,125] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:03:56,125] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:03:56,125] [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 06:03:56,126] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38100/tc_result.tsv
[2023-03-16 06:03:56,126] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:03:56,126] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:03:56,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference/checkm_data
[2023-03-16 06:03:56,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:03:56,151] [INFO] Task started: CheckM
[2023-03-16 06:03:56,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38100/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38100/checkm_input OceanDNA-b38100/checkm_result
[2023-03-16 06:04:33,393] [INFO] Task succeeded: CheckM
[2023-03-16 06:04:33,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:04:33,539] [INFO] ===== Completeness check finished =====
[2023-03-16 06:04:33,539] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:04:33,539] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38100/markers.fasta)
[2023-03-16 06:04:33,541] [INFO] Task started: Blastn
[2023-03-16 06:04:33,541] [INFO] Running command: blastn -query OceanDNA-b38100/markers.fasta -db /var/lib/cwl/stge0bd0ab5-9973-42ae-aa07-4ea1508cb9bc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38100/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:04:34,391] [INFO] Task succeeded: Blastn
[2023-03-16 06:04:34,392] [INFO] Selected 16 target genomes.
[2023-03-16 06:04:34,392] [INFO] Target genome list was writen to OceanDNA-b38100/target_genomes_gtdb.txt
[2023-03-16 06:04:34,431] [INFO] Task started: fastANI
[2023-03-16 06:04:34,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgbefabd7a-bcc1-40f1-a934-28209a7b4ffe/OceanDNA-b38100.fa --refList OceanDNA-b38100/target_genomes_gtdb.txt --output OceanDNA-b38100/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:04:41,743] [INFO] Task succeeded: fastANI
[2023-03-16 06:04:41,748] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:04:41,748] [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_002683395.1	s__Luminiphilus sp002683395	96.3264	528	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	conclusive
GCA_018222695.1	s__Luminiphilus sp018222695	78.6149	191	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	78.4594	178	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518075.1	s__Luminiphilus sp902518075	78.0777	96	738	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	77.9013	117	738	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	77.8309	175	738	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_016778045.1	s__Luminiphilus sp016778045	77.7823	150	738	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	77.3539	175	738	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 06:04:41,748] [INFO] GTDB search result was written to OceanDNA-b38100/result_gtdb.tsv
[2023-03-16 06:04:41,748] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:04:41,749] [INFO] DFAST_QC result json was written to OceanDNA-b38100/dqc_result.json
[2023-03-16 06:04:41,749] [INFO] DFAST_QC completed!
[2023-03-16 06:04:41,749] [INFO] Total running time: 0h1m16s