[2023-03-15 21:32:41,291] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:32:41,291] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:32:41,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference
[2023-03-15 21:32:42,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:32:42,946] [INFO] Task started: Prodigal
[2023-03-15 21:32:42,946] [INFO] Running command: cat /var/lib/cwl/stg266d4495-0400-454e-bafd-9fefe3110589/OceanDNA-b1965.fa | prodigal -d OceanDNA-b1965/cds.fna -a OceanDNA-b1965/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:32:48,712] [INFO] Task succeeded: Prodigal
[2023-03-15 21:32:48,713] [INFO] Task started: HMMsearch
[2023-03-15 21:32:48,713] [INFO] Running command: hmmsearch --tblout OceanDNA-b1965/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference/reference_markers.hmm OceanDNA-b1965/protein.faa > /dev/null
[2023-03-15 21:32:48,848] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:32:48,849] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg266d4495-0400-454e-bafd-9fefe3110589/OceanDNA-b1965.fa]
[2023-03-15 21:32:48,858] [INFO] Query marker FASTA was written to OceanDNA-b1965/markers.fasta
[2023-03-15 21:32:48,858] [INFO] Task started: Blastn
[2023-03-15 21:32:48,858] [INFO] Running command: blastn -query OceanDNA-b1965/markers.fasta -db /var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference/reference_markers.fasta -out OceanDNA-b1965/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:32:49,337] [INFO] Task succeeded: Blastn
[2023-03-15 21:32:49,338] [INFO] Selected 7 target genomes.
[2023-03-15 21:32:49,338] [INFO] Target genome list was writen to OceanDNA-b1965/target_genomes.txt
[2023-03-15 21:32:49,369] [INFO] Task started: fastANI
[2023-03-15 21:32:49,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg266d4495-0400-454e-bafd-9fefe3110589/OceanDNA-b1965.fa --refList OceanDNA-b1965/target_genomes.txt --output OceanDNA-b1965/fastani_result.tsv --threads 1
[2023-03-15 21:32:53,197] [INFO] Task succeeded: fastANI
[2023-03-15 21:32:53,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:32:53,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:32:53,198] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:32:53,198] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:32:53,198] [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 21:32:53,198] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1965/tc_result.tsv
[2023-03-15 21:32:53,198] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:32:53,198] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:32:53,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference/checkm_data
[2023-03-15 21:32:53,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:32:53,203] [INFO] Task started: CheckM
[2023-03-15 21:32:53,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1965/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1965/checkm_input OceanDNA-b1965/checkm_result
[2023-03-15 21:33:14,763] [INFO] Task succeeded: CheckM
[2023-03-15 21:33:14,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:33:14,765] [INFO] ===== Completeness check finished =====
[2023-03-15 21:33:14,765] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:33:14,765] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1965/markers.fasta)
[2023-03-15 21:33:14,765] [INFO] Task started: Blastn
[2023-03-15 21:33:14,765] [INFO] Running command: blastn -query OceanDNA-b1965/markers.fasta -db /var/lib/cwl/stg63f68097-cd47-48e5-8649-60a8ed990e36/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1965/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:33:16,061] [INFO] Task succeeded: Blastn
[2023-03-15 21:33:16,063] [INFO] Selected 13 target genomes.
[2023-03-15 21:33:16,063] [INFO] Target genome list was writen to OceanDNA-b1965/target_genomes_gtdb.txt
[2023-03-15 21:33:16,669] [INFO] Task started: fastANI
[2023-03-15 21:33:16,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg266d4495-0400-454e-bafd-9fefe3110589/OceanDNA-b1965.fa --refList OceanDNA-b1965/target_genomes_gtdb.txt --output OceanDNA-b1965/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:33:21,983] [INFO] Task succeeded: fastANI
[2023-03-15 21:33:21,988] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:33:21,988] [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_002715425.1	s__UBA8592 sp002715425	98.7184	221	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002703045.1	s__UBA8592 sp002703045	89.4615	243	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	95.31	95.20	0.70	0.69	3	-
GCA_002722525.1	s__UBA8592 sp002722525	89.2512	230	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.15	99.15	0.66	0.66	2	-
GCA_002724825.1	s__UBA8592 sp002724825	89.1217	256	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	98.36	98.27	0.75	0.75	3	-
GCA_902565595.1	s__UBA8592 sp902565595	81.4518	154	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720485.1	s__UBA8592 sp002720485	81.2524	174	346	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	96.65	96.65	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:33:21,988] [INFO] GTDB search result was written to OceanDNA-b1965/result_gtdb.tsv
[2023-03-15 21:33:21,989] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:33:21,989] [INFO] DFAST_QC result json was written to OceanDNA-b1965/dqc_result.json
[2023-03-15 21:33:21,989] [INFO] DFAST_QC completed!
[2023-03-15 21:33:21,989] [INFO] Total running time: 0h0m41s