[2023-03-19 00:54:54,754] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:54:54,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:54:54,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference
[2023-03-19 00:54:55,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:54:55,892] [INFO] Task started: Prodigal
[2023-03-19 00:54:55,892] [INFO] Running command: cat /var/lib/cwl/stgce559eac-d2b2-45dc-87cd-b936b232655d/OceanDNA-b45289.fa | prodigal -d OceanDNA-b45289/cds.fna -a OceanDNA-b45289/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:55:12,300] [INFO] Task succeeded: Prodigal
[2023-03-19 00:55:12,301] [INFO] Task started: HMMsearch
[2023-03-19 00:55:12,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b45289/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference/reference_markers.hmm OceanDNA-b45289/protein.faa > /dev/null
[2023-03-19 00:55:12,483] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:55:12,484] [INFO] Found 6/6 markers.
[2023-03-19 00:55:12,539] [INFO] Query marker FASTA was written to OceanDNA-b45289/markers.fasta
[2023-03-19 00:55:12,540] [INFO] Task started: Blastn
[2023-03-19 00:55:12,540] [INFO] Running command: blastn -query OceanDNA-b45289/markers.fasta -db /var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference/reference_markers.fasta -out OceanDNA-b45289/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:55:13,135] [INFO] Task succeeded: Blastn
[2023-03-19 00:55:13,140] [INFO] Selected 30 target genomes.
[2023-03-19 00:55:13,141] [INFO] Target genome list was writen to OceanDNA-b45289/target_genomes.txt
[2023-03-19 00:55:13,157] [INFO] Task started: fastANI
[2023-03-19 00:55:13,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgce559eac-d2b2-45dc-87cd-b936b232655d/OceanDNA-b45289.fa --refList OceanDNA-b45289/target_genomes.txt --output OceanDNA-b45289/fastani_result.tsv --threads 1
[2023-03-19 00:55:32,665] [INFO] Task succeeded: fastANI
[2023-03-19 00:55:32,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:55:32,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:55:32,666] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:55:32,666] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:55:32,666] [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
--------------------------------------------------------------------------------
[2023-03-19 00:55:32,672] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45289/tc_result.tsv
[2023-03-19 00:55:32,682] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:55:32,683] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:55:32,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference/checkm_data
[2023-03-19 00:55:32,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:55:32,691] [INFO] Task started: CheckM
[2023-03-19 00:55:32,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45289/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45289/checkm_input OceanDNA-b45289/checkm_result
[2023-03-19 00:56:15,417] [INFO] Task succeeded: CheckM
[2023-03-19 00:56:15,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:56:15,468] [INFO] ===== Completeness check finished =====
[2023-03-19 00:56:15,468] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:56:15,468] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45289/markers.fasta)
[2023-03-19 00:56:15,469] [INFO] Task started: Blastn
[2023-03-19 00:56:15,469] [INFO] Running command: blastn -query OceanDNA-b45289/markers.fasta -db /var/lib/cwl/stg10128dee-5dbe-44db-b344-c44e200c56ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45289/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:56:16,417] [INFO] Task succeeded: Blastn
[2023-03-19 00:56:16,439] [INFO] Selected 26 target genomes.
[2023-03-19 00:56:16,439] [INFO] Target genome list was writen to OceanDNA-b45289/target_genomes_gtdb.txt
[2023-03-19 00:56:16,472] [INFO] Task started: fastANI
[2023-03-19 00:56:16,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgce559eac-d2b2-45dc-87cd-b936b232655d/OceanDNA-b45289.fa --refList OceanDNA-b45289/target_genomes_gtdb.txt --output OceanDNA-b45289/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:56:30,265] [INFO] Task succeeded: fastANI
[2023-03-19 00:56:30,270] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:56:30,270] [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_002685755.1	s__UBA8248 sp002685755	98.6308	572	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__UBA8248	95.0	98.93	98.93	0.70	0.70	2	conclusive
GCA_018669005.1	s__UBA8248 sp018669005	77.7951	267	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__UBA8248	95.0	99.88	99.83	0.95	0.94	9	-
GCA_001790955.1	s__2-12-FULL-69-37 sp001790955	77.0888	185	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	99.54	99.54	0.87	0.87	2	-
GCA_016192135.1	s__2-12-FULL-69-37 sp016192135	77.065	190	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__2-12-FULL-69-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839615.1	s__Bin107 sp009839615	76.7052	116	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238965.1	s__Bin107 sp002238965	76.5288	121	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523725.1	s__Bin107 sp011523725	76.4745	101	922	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:56:30,272] [INFO] GTDB search result was written to OceanDNA-b45289/result_gtdb.tsv
[2023-03-19 00:56:30,274] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:56:30,277] [INFO] DFAST_QC result json was written to OceanDNA-b45289/dqc_result.json
[2023-03-19 00:56:30,277] [INFO] DFAST_QC completed!
[2023-03-19 00:56:30,277] [INFO] Total running time: 0h1m36s