[2023-03-15 17:24:01,281] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,282] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,282] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference
[2023-03-15 17:24:02,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,514] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,515] [INFO] Running command: cat /var/lib/cwl/stgcd8964e7-03ee-4082-911d-63c0843a4ca6/OceanDNA-b1931.fa | prodigal -d OceanDNA-b1931/cds.fna -a OceanDNA-b1931/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:11,066] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:11,067] [INFO] Task started: HMMsearch
[2023-03-15 17:24:11,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b1931/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference/reference_markers.hmm OceanDNA-b1931/protein.faa > /dev/null
[2023-03-15 17:24:11,373] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:11,373] [INFO] Found 6/6 markers.
[2023-03-15 17:24:11,387] [INFO] Query marker FASTA was written to OceanDNA-b1931/markers.fasta
[2023-03-15 17:24:11,401] [INFO] Task started: Blastn
[2023-03-15 17:24:11,401] [INFO] Running command: blastn -query OceanDNA-b1931/markers.fasta -db /var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference/reference_markers.fasta -out OceanDNA-b1931/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:11,959] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:11,960] [INFO] Selected 16 target genomes.
[2023-03-15 17:24:11,960] [INFO] Target genome list was writen to OceanDNA-b1931/target_genomes.txt
[2023-03-15 17:24:11,971] [INFO] Task started: fastANI
[2023-03-15 17:24:11,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd8964e7-03ee-4082-911d-63c0843a4ca6/OceanDNA-b1931.fa --refList OceanDNA-b1931/target_genomes.txt --output OceanDNA-b1931/fastani_result.tsv --threads 1
[2023-03-15 17:24:19,414] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:19,415] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:19,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:19,415] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:19,415] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:24:19,415] [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 17:24:19,415] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1931/tc_result.tsv
[2023-03-15 17:24:19,416] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:19,416] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:19,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference/checkm_data
[2023-03-15 17:24:19,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:19,422] [INFO] Task started: CheckM
[2023-03-15 17:24:19,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1931/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1931/checkm_input OceanDNA-b1931/checkm_result
[2023-03-15 17:24:46,700] [INFO] Task succeeded: CheckM
[2023-03-15 17:24:46,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 5.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-15 17:24:46,702] [INFO] ===== Completeness check finished =====
[2023-03-15 17:24:46,702] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:24:46,702] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1931/markers.fasta)
[2023-03-15 17:24:46,703] [INFO] Task started: Blastn
[2023-03-15 17:24:46,704] [INFO] Running command: blastn -query OceanDNA-b1931/markers.fasta -db /var/lib/cwl/stgb3187d06-bcd4-452f-b428-768a5ce4da69/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1931/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:47,636] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:47,637] [INFO] Selected 12 target genomes.
[2023-03-15 17:24:47,637] [INFO] Target genome list was writen to OceanDNA-b1931/target_genomes_gtdb.txt
[2023-03-15 17:24:47,650] [INFO] Task started: fastANI
[2023-03-15 17:24:47,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd8964e7-03ee-4082-911d-63c0843a4ca6/OceanDNA-b1931.fa --refList OceanDNA-b1931/target_genomes_gtdb.txt --output OceanDNA-b1931/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:24:51,521] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:51,525] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:24:51,526] [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_002713605.1	s__UBA8592 sp002713605	97.9656	148	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.46	99.46	0.60	0.60	2	conclusive
GCA_002295705.1	s__UBA8592 sp002295705	88.882	378	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.20	99.08	0.80	0.73	4	-
GCA_011523005.1	s__UBA8592 sp002380145	86.5556	396	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.37	95.83	0.82	0.81	6	-
GCA_002712415.1	s__UBA8592 sp002712415	85.3396	303	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.66	97.33	0.73	0.67	3	-
GCA_002712325.1	s__UBA8592 sp002712325	83.6642	241	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.19	99.19	0.77	0.77	2	-
GCA_002341185.1	s__UBA8592 sp002341185	80.7	261	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.95	99.95	0.96	0.96	2	-
GCA_002713485.1	s__UBA8592 sp002713485	80.1239	127	507	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.04	97.04	0.72	0.72	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:24:51,526] [INFO] GTDB search result was written to OceanDNA-b1931/result_gtdb.tsv
[2023-03-15 17:24:51,526] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:24:51,527] [INFO] DFAST_QC result json was written to OceanDNA-b1931/dqc_result.json
[2023-03-15 17:24:51,527] [INFO] DFAST_QC completed!
[2023-03-15 17:24:51,527] [INFO] Total running time: 0h0m50s