[2023-03-18 23:11:06,984] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,984] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,984] [INFO] DQC Reference Directory: /var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference
[2023-03-18 23:11:08,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,166] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,166] [INFO] Running command: cat /var/lib/cwl/stgfb02a4e7-ba24-4144-a503-8533a6978d89/OceanDNA-b16882.fa | prodigal -d OceanDNA-b16882/cds.fna -a OceanDNA-b16882/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:11,691] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:11,691] [INFO] Task started: HMMsearch
[2023-03-18 23:11:11,692] [INFO] Running command: hmmsearch --tblout OceanDNA-b16882/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference/reference_markers.hmm OceanDNA-b16882/protein.faa > /dev/null
[2023-03-18 23:11:11,855] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:11,855] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfb02a4e7-ba24-4144-a503-8533a6978d89/OceanDNA-b16882.fa]
[2023-03-18 23:11:11,861] [INFO] Query marker FASTA was written to OceanDNA-b16882/markers.fasta
[2023-03-18 23:11:11,862] [INFO] Task started: Blastn
[2023-03-18 23:11:11,862] [INFO] Running command: blastn -query OceanDNA-b16882/markers.fasta -db /var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference/reference_markers.fasta -out OceanDNA-b16882/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:12,340] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:12,341] [INFO] Selected 17 target genomes.
[2023-03-18 23:11:12,341] [INFO] Target genome list was writen to OceanDNA-b16882/target_genomes.txt
[2023-03-18 23:11:12,349] [INFO] Task started: fastANI
[2023-03-18 23:11:12,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb02a4e7-ba24-4144-a503-8533a6978d89/OceanDNA-b16882.fa --refList OceanDNA-b16882/target_genomes.txt --output OceanDNA-b16882/fastani_result.tsv --threads 1
[2023-03-18 23:11:21,347] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:21,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:21,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:21,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:21,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:11:21,348] [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
--------------------------------------------------------------------------------
[2023-03-18 23:11:21,349] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16882/tc_result.tsv
[2023-03-18 23:11:21,349] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:21,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:21,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference/checkm_data
[2023-03-18 23:11:21,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:21,356] [INFO] Task started: CheckM
[2023-03-18 23:11:21,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16882/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16882/checkm_input OceanDNA-b16882/checkm_result
[2023-03-18 23:11:36,723] [INFO] Task succeeded: CheckM
[2023-03-18 23:11:36,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:11:36,725] [INFO] ===== Completeness check finished =====
[2023-03-18 23:11:36,725] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:11:36,725] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16882/markers.fasta)
[2023-03-18 23:11:36,725] [INFO] Task started: Blastn
[2023-03-18 23:11:36,725] [INFO] Running command: blastn -query OceanDNA-b16882/markers.fasta -db /var/lib/cwl/stgca962f54-3421-4593-86d5-62177e63d82b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16882/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:37,390] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:37,390] [INFO] Selected 12 target genomes.
[2023-03-18 23:11:37,391] [INFO] Target genome list was writen to OceanDNA-b16882/target_genomes_gtdb.txt
[2023-03-18 23:11:37,407] [INFO] Task started: fastANI
[2023-03-18 23:11:37,407] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb02a4e7-ba24-4144-a503-8533a6978d89/OceanDNA-b16882.fa --refList OceanDNA-b16882/target_genomes_gtdb.txt --output OceanDNA-b16882/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:11:40,792] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:40,796] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:11:40,796] [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_002715585.2	s__GCA-002715585 sp002715585	99.4509	221	234	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-002715585	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902609885.1	s__GCA-002715585 sp902609885	92.9179	213	234	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-002715585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697665.2	s__GCA-002715585 sp002697665	87.7085	189	234	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__GCA-002715585	95.0	96.81	96.81	0.86	0.86	2	-
GCA_002701605.2	s__TMED126 sp002701605	77.514	72	234	d__Bacteria;p__Desulfobacterota_D;c__UBA1144;o__UBA1144;f__UBA1144;g__TMED126	95.0	95.74	95.73	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:11:40,796] [INFO] GTDB search result was written to OceanDNA-b16882/result_gtdb.tsv
[2023-03-18 23:11:40,796] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:11:40,797] [INFO] DFAST_QC result json was written to OceanDNA-b16882/dqc_result.json
[2023-03-18 23:11:40,797] [INFO] DFAST_QC completed!
[2023-03-18 23:11:40,797] [INFO] Total running time: 0h0m34s