[2023-03-17 08:56:41,432] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:56:41,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:56:41,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference
[2023-03-17 08:56:42,668] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:56:42,669] [INFO] Task started: Prodigal
[2023-03-17 08:56:42,669] [INFO] Running command: cat /var/lib/cwl/stge44df029-ab1e-490f-a20a-b4becdb1832a/OceanDNA-b42477.fa | prodigal -d OceanDNA-b42477/cds.fna -a OceanDNA-b42477/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:56:48,663] [INFO] Task succeeded: Prodigal
[2023-03-17 08:56:48,663] [INFO] Task started: HMMsearch
[2023-03-17 08:56:48,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b42477/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference/reference_markers.hmm OceanDNA-b42477/protein.faa > /dev/null
[2023-03-17 08:56:48,829] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:56:48,830] [INFO] Found 6/6 markers.
[2023-03-17 08:56:48,851] [INFO] Query marker FASTA was written to OceanDNA-b42477/markers.fasta
[2023-03-17 08:56:48,853] [INFO] Task started: Blastn
[2023-03-17 08:56:48,853] [INFO] Running command: blastn -query OceanDNA-b42477/markers.fasta -db /var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference/reference_markers.fasta -out OceanDNA-b42477/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:56:49,346] [INFO] Task succeeded: Blastn
[2023-03-17 08:56:49,347] [INFO] Selected 15 target genomes.
[2023-03-17 08:56:49,347] [INFO] Target genome list was writen to OceanDNA-b42477/target_genomes.txt
[2023-03-17 08:56:49,455] [INFO] Task started: fastANI
[2023-03-17 08:56:49,455] [INFO] Running command: fastANI --query /var/lib/cwl/stge44df029-ab1e-490f-a20a-b4becdb1832a/OceanDNA-b42477.fa --refList OceanDNA-b42477/target_genomes.txt --output OceanDNA-b42477/fastani_result.tsv --threads 1
[2023-03-17 08:56:56,117] [INFO] Task succeeded: fastANI
[2023-03-17 08:56:56,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:56:56,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:56:56,118] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:56:56,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:56:56,118] [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
--------------------------------------------------------------------------------
[2023-03-17 08:56:56,121] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42477/tc_result.tsv
[2023-03-17 08:56:56,127] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:56:56,127] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:56:56,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference/checkm_data
[2023-03-17 08:56:56,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:56:56,252] [INFO] Task started: CheckM
[2023-03-17 08:56:56,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42477/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42477/checkm_input OceanDNA-b42477/checkm_result
[2023-03-17 08:57:22,255] [INFO] Task succeeded: CheckM
[2023-03-17 08:57:22,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:57:22,270] [INFO] ===== Completeness check finished =====
[2023-03-17 08:57:22,270] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:57:22,270] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42477/markers.fasta)
[2023-03-17 08:57:22,270] [INFO] Task started: Blastn
[2023-03-17 08:57:22,270] [INFO] Running command: blastn -query OceanDNA-b42477/markers.fasta -db /var/lib/cwl/stg64b9dc14-f7af-47c3-903a-cdc7f9b6ac60/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42477/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:57:23,423] [INFO] Task succeeded: Blastn
[2023-03-17 08:57:23,428] [INFO] Selected 23 target genomes.
[2023-03-17 08:57:23,428] [INFO] Target genome list was writen to OceanDNA-b42477/target_genomes_gtdb.txt
[2023-03-17 08:57:24,150] [INFO] Task started: fastANI
[2023-03-17 08:57:24,150] [INFO] Running command: fastANI --query /var/lib/cwl/stge44df029-ab1e-490f-a20a-b4becdb1832a/OceanDNA-b42477.fa --refList OceanDNA-b42477/target_genomes_gtdb.txt --output OceanDNA-b42477/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:57:30,172] [INFO] Task succeeded: fastANI
[2023-03-17 08:57:30,175] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:57:30,175] [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_012965075.1	s__AEGEAN-183 sp012965075	97.1977	270	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	98.73	98.73	0.80	0.80	2	conclusive
GCA_001628005.1	s__AEGEAN-183 sp001628005	79.5836	237	383	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__AEGEAN-183	95.0	99.32	99.31	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 08:57:30,177] [INFO] GTDB search result was written to OceanDNA-b42477/result_gtdb.tsv
[2023-03-17 08:57:30,179] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:57:30,181] [INFO] DFAST_QC result json was written to OceanDNA-b42477/dqc_result.json
[2023-03-17 08:57:30,181] [INFO] DFAST_QC completed!
[2023-03-17 08:57:30,182] [INFO] Total running time: 0h0m49s