[2023-03-15 03:14:16,347] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference
[2023-03-15 03:14:17,498] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,499] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,499] [INFO] Running command: cat /var/lib/cwl/stg37c89031-578e-4e6d-afdd-df25699b4dc6/OceanDNA-b42746.fa | prodigal -d OceanDNA-b42746/cds.fna -a OceanDNA-b42746/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:23,318] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:23,319] [INFO] Task started: HMMsearch
[2023-03-15 03:14:23,319] [INFO] Running command: hmmsearch --tblout OceanDNA-b42746/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference/reference_markers.hmm OceanDNA-b42746/protein.faa > /dev/null
[2023-03-15 03:14:23,478] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:23,479] [INFO] Found 6/6 markers.
[2023-03-15 03:14:23,486] [INFO] Query marker FASTA was written to OceanDNA-b42746/markers.fasta
[2023-03-15 03:14:23,486] [INFO] Task started: Blastn
[2023-03-15 03:14:23,486] [INFO] Running command: blastn -query OceanDNA-b42746/markers.fasta -db /var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference/reference_markers.fasta -out OceanDNA-b42746/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:23,980] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:23,981] [INFO] Selected 15 target genomes.
[2023-03-15 03:14:23,981] [INFO] Target genome list was writen to OceanDNA-b42746/target_genomes.txt
[2023-03-15 03:14:23,988] [INFO] Task started: fastANI
[2023-03-15 03:14:23,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg37c89031-578e-4e6d-afdd-df25699b4dc6/OceanDNA-b42746.fa --refList OceanDNA-b42746/target_genomes.txt --output OceanDNA-b42746/fastani_result.tsv --threads 1
[2023-03-15 03:14:29,226] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:29,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:29,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:29,227] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:29,227] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:14:29,227] [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
--------------------------------------------------------------------------------
[2023-03-15 03:14:29,227] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42746/tc_result.tsv
[2023-03-15 03:14:29,227] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:29,228] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:29,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference/checkm_data
[2023-03-15 03:14:29,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:29,233] [INFO] Task started: CheckM
[2023-03-15 03:14:29,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42746/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42746/checkm_input OceanDNA-b42746/checkm_result
[2023-03-15 03:14:50,343] [INFO] Task succeeded: CheckM
[2023-03-15 03:14:50,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:14:50,345] [INFO] ===== Completeness check finished =====
[2023-03-15 03:14:50,345] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:14:50,345] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42746/markers.fasta)
[2023-03-15 03:14:50,345] [INFO] Task started: Blastn
[2023-03-15 03:14:50,345] [INFO] Running command: blastn -query OceanDNA-b42746/markers.fasta -db /var/lib/cwl/stg453dd608-426f-41d5-881b-3cab67b130f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42746/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:51,049] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:51,050] [INFO] Selected 15 target genomes.
[2023-03-15 03:14:51,050] [INFO] Target genome list was writen to OceanDNA-b42746/target_genomes_gtdb.txt
[2023-03-15 03:14:51,096] [INFO] Task started: fastANI
[2023-03-15 03:14:51,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg37c89031-578e-4e6d-afdd-df25699b4dc6/OceanDNA-b42746.fa --refList OceanDNA-b42746/target_genomes_gtdb.txt --output OceanDNA-b42746/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:14:54,229] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:54,233] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:14:54,233] [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_902563885.1	s__TMED112 sp902563885	95.2178	267	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.04	95.25	0.89	0.85	3	conclusive
GCA_003280455.1	s__TMED112 sp003280455	94.9976	252	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.03	95.13	0.84	0.71	14	-
GCA_902526535.1	s__TMED112 sp902526535	91.1978	207	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002716745.1	s__TMED112 sp002716745	77.0033	54	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.67	96.57	0.91	0.90	3	-
GCA_003278815.1	s__TMED112 sp003278815	76.8597	54	308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:14:54,234] [INFO] GTDB search result was written to OceanDNA-b42746/result_gtdb.tsv
[2023-03-15 03:14:54,234] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:14:54,234] [INFO] DFAST_QC result json was written to OceanDNA-b42746/dqc_result.json
[2023-03-15 03:14:54,235] [INFO] DFAST_QC completed!
[2023-03-15 03:14:54,235] [INFO] Total running time: 0h0m38s