[2023-03-15 22:25:05,311] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:25:05,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:25:05,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference
[2023-03-15 22:25:06,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:25:06,473] [INFO] Task started: Prodigal
[2023-03-15 22:25:06,473] [INFO] Running command: cat /var/lib/cwl/stg42d24ce0-6549-45c6-bc8f-f77abcbb8dcc/OceanDNA-b5502.fa | prodigal -d OceanDNA-b5502/cds.fna -a OceanDNA-b5502/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:25:19,039] [INFO] Task succeeded: Prodigal
[2023-03-15 22:25:19,039] [INFO] Task started: HMMsearch
[2023-03-15 22:25:19,039] [INFO] Running command: hmmsearch --tblout OceanDNA-b5502/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference/reference_markers.hmm OceanDNA-b5502/protein.faa > /dev/null
[2023-03-15 22:25:19,212] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:25:19,213] [INFO] Found 6/6 markers.
[2023-03-15 22:25:19,229] [INFO] Query marker FASTA was written to OceanDNA-b5502/markers.fasta
[2023-03-15 22:25:19,229] [INFO] Task started: Blastn
[2023-03-15 22:25:19,229] [INFO] Running command: blastn -query OceanDNA-b5502/markers.fasta -db /var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference/reference_markers.fasta -out OceanDNA-b5502/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:25:19,803] [INFO] Task succeeded: Blastn
[2023-03-15 22:25:19,804] [INFO] Selected 19 target genomes.
[2023-03-15 22:25:19,804] [INFO] Target genome list was writen to OceanDNA-b5502/target_genomes.txt
[2023-03-15 22:25:19,814] [INFO] Task started: fastANI
[2023-03-15 22:25:19,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg42d24ce0-6549-45c6-bc8f-f77abcbb8dcc/OceanDNA-b5502.fa --refList OceanDNA-b5502/target_genomes.txt --output OceanDNA-b5502/fastani_result.tsv --threads 1
[2023-03-15 22:25:31,092] [INFO] Task succeeded: fastANI
[2023-03-15 22:25:31,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:25:31,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:25:31,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:25:31,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:25:31,093] [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 22:25:31,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5502/tc_result.tsv
[2023-03-15 22:25:31,093] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:25:31,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:25:31,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference/checkm_data
[2023-03-15 22:25:31,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:25:31,205] [INFO] Task started: CheckM
[2023-03-15 22:25:31,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5502/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5502/checkm_input OceanDNA-b5502/checkm_result
[2023-03-15 22:26:07,382] [INFO] Task succeeded: CheckM
[2023-03-15 22:26:07,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:26:07,385] [INFO] ===== Completeness check finished =====
[2023-03-15 22:26:07,385] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:26:07,386] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5502/markers.fasta)
[2023-03-15 22:26:07,386] [INFO] Task started: Blastn
[2023-03-15 22:26:07,386] [INFO] Running command: blastn -query OceanDNA-b5502/markers.fasta -db /var/lib/cwl/stgdfa3e36b-b40e-4e1a-b8f3-c96113f3e393/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5502/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:26:08,339] [INFO] Task succeeded: Blastn
[2023-03-15 22:26:08,340] [INFO] Selected 22 target genomes.
[2023-03-15 22:26:08,340] [INFO] Target genome list was writen to OceanDNA-b5502/target_genomes_gtdb.txt
[2023-03-15 22:26:08,466] [INFO] Task started: fastANI
[2023-03-15 22:26:08,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg42d24ce0-6549-45c6-bc8f-f77abcbb8dcc/OceanDNA-b5502.fa --refList OceanDNA-b5502/target_genomes_gtdb.txt --output OceanDNA-b5502/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:26:17,368] [INFO] Task succeeded: fastANI
[2023-03-15 22:26:17,373] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:26:17,373] [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_003331365.1	s__UBA952 sp003331365	99.4798	371	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011522905.1	s__UBA952 sp011522905	92.392	380	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480165.1	s__UBA952 sp905480165	78.1964	187	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665005.1	s__UBA952 sp018665005	77.7811	185	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.77	98.77	0.77	0.77	2	-
GCA_002167775.1	s__UBA952 sp002167775	76.6578	80	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
GCA_002480215.1	s__UBA952 sp002480215	76.4695	68	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_905182495.1	s__UBA952 sp905182495	76.3475	62	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:26:17,374] [INFO] GTDB search result was written to OceanDNA-b5502/result_gtdb.tsv
[2023-03-15 22:26:17,374] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:26:17,375] [INFO] DFAST_QC result json was written to OceanDNA-b5502/dqc_result.json
[2023-03-15 22:26:17,375] [INFO] DFAST_QC completed!
[2023-03-15 22:26:17,375] [INFO] Total running time: 0h1m12s