[2023-03-14 11:13:58,988] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,988] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,988] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference
[2023-03-14 11:14:00,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,598] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,598] [INFO] Running command: cat /var/lib/cwl/stgbea94dc7-e2ef-42d6-acc4-08ea2b7e5fbf/OceanDNA-b45284.fa | prodigal -d OceanDNA-b45284/cds.fna -a OceanDNA-b45284/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:13,082] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:13,082] [INFO] Task started: HMMsearch
[2023-03-14 11:14:13,082] [INFO] Running command: hmmsearch --tblout OceanDNA-b45284/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference/reference_markers.hmm OceanDNA-b45284/protein.faa > /dev/null
[2023-03-14 11:14:13,262] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:13,262] [INFO] Found 6/6 markers.
[2023-03-14 11:14:13,280] [INFO] Query marker FASTA was written to OceanDNA-b45284/markers.fasta
[2023-03-14 11:14:13,282] [INFO] Task started: Blastn
[2023-03-14 11:14:13,282] [INFO] Running command: blastn -query OceanDNA-b45284/markers.fasta -db /var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference/reference_markers.fasta -out OceanDNA-b45284/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:13,832] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:13,833] [INFO] Selected 19 target genomes.
[2023-03-14 11:14:13,833] [INFO] Target genome list was writen to OceanDNA-b45284/target_genomes.txt
[2023-03-14 11:14:13,845] [INFO] Task started: fastANI
[2023-03-14 11:14:13,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea94dc7-e2ef-42d6-acc4-08ea2b7e5fbf/OceanDNA-b45284.fa --refList OceanDNA-b45284/target_genomes.txt --output OceanDNA-b45284/fastani_result.tsv --threads 1
[2023-03-14 11:14:26,043] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:26,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:26,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:26,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:26,044] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:14:26,044] [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
--------------------------------------------------------------------------------
[2023-03-14 11:14:26,044] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45284/tc_result.tsv
[2023-03-14 11:14:26,045] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:26,045] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:26,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference/checkm_data
[2023-03-14 11:14:26,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:26,051] [INFO] Task started: CheckM
[2023-03-14 11:14:26,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45284/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45284/checkm_input OceanDNA-b45284/checkm_result
[2023-03-14 11:15:00,823] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:00,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:00,825] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:00,825] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:00,825] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45284/markers.fasta)
[2023-03-14 11:15:00,827] [INFO] Task started: Blastn
[2023-03-14 11:15:00,827] [INFO] Running command: blastn -query OceanDNA-b45284/markers.fasta -db /var/lib/cwl/stgc4ccae3d-0a5c-4d31-872e-7730e34b2a25/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45284/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:01,692] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:01,693] [INFO] Selected 22 target genomes.
[2023-03-14 11:15:01,693] [INFO] Target genome list was writen to OceanDNA-b45284/target_genomes_gtdb.txt
[2023-03-14 11:15:01,719] [INFO] Task started: fastANI
[2023-03-14 11:15:01,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgbea94dc7-e2ef-42d6-acc4-08ea2b7e5fbf/OceanDNA-b45284.fa --refList OceanDNA-b45284/target_genomes_gtdb.txt --output OceanDNA-b45284/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:14,539] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:14,542] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:14,542] [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_018669005.1	s__UBA8248 sp018669005	83.0083	580	684	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__UBA8248	95.0	99.88	99.83	0.95	0.94	9	-
GCA_009839615.1	s__Bin107 sp009839615	76.4496	55	684	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	75.6869	50	684	d__Bacteria;p__UBA8248;c__UBA8248;o__UBA8248;f__UBA8248;g__Bin107	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:14,542] [INFO] GTDB search result was written to OceanDNA-b45284/result_gtdb.tsv
[2023-03-14 11:15:14,542] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:14,542] [INFO] DFAST_QC result json was written to OceanDNA-b45284/dqc_result.json
[2023-03-14 11:15:14,543] [INFO] DFAST_QC completed!
[2023-03-14 11:15:14,543] [INFO] Total running time: 0h1m16s