[2023-03-15 13:03:55,414] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:55,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:55,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference
[2023-03-15 13:03:56,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:56,706] [INFO] Task started: Prodigal
[2023-03-15 13:03:56,706] [INFO] Running command: cat /var/lib/cwl/stgb11fb6c2-2c96-46c5-afa7-9d88b9d868d8/OceanDNA-b17690.fa | prodigal -d OceanDNA-b17690/cds.fna -a OceanDNA-b17690/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:07,078] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:07,079] [INFO] Task started: HMMsearch
[2023-03-15 13:04:07,079] [INFO] Running command: hmmsearch --tblout OceanDNA-b17690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference/reference_markers.hmm OceanDNA-b17690/protein.faa > /dev/null
[2023-03-15 13:04:07,321] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:07,322] [INFO] Found 6/6 markers.
[2023-03-15 13:04:07,348] [INFO] Query marker FASTA was written to OceanDNA-b17690/markers.fasta
[2023-03-15 13:04:07,348] [INFO] Task started: Blastn
[2023-03-15 13:04:07,349] [INFO] Running command: blastn -query OceanDNA-b17690/markers.fasta -db /var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference/reference_markers.fasta -out OceanDNA-b17690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:07,884] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:07,885] [INFO] Selected 21 target genomes.
[2023-03-15 13:04:07,885] [INFO] Target genome list was writen to OceanDNA-b17690/target_genomes.txt
[2023-03-15 13:04:07,899] [INFO] Task started: fastANI
[2023-03-15 13:04:07,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgb11fb6c2-2c96-46c5-afa7-9d88b9d868d8/OceanDNA-b17690.fa --refList OceanDNA-b17690/target_genomes.txt --output OceanDNA-b17690/fastani_result.tsv --threads 1
[2023-03-15 13:04:23,728] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:23,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:23,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:23,728] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:23,728] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:04:23,728] [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 13:04:23,729] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17690/tc_result.tsv
[2023-03-15 13:04:23,729] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:23,729] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:23,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference/checkm_data
[2023-03-15 13:04:23,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:23,736] [INFO] Task started: CheckM
[2023-03-15 13:04:23,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17690/checkm_input OceanDNA-b17690/checkm_result
[2023-03-15 13:04:54,624] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:54,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:54,627] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:54,627] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:54,628] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17690/markers.fasta)
[2023-03-15 13:04:54,628] [INFO] Task started: Blastn
[2023-03-15 13:04:54,628] [INFO] Running command: blastn -query OceanDNA-b17690/markers.fasta -db /var/lib/cwl/stg363624ce-ff25-49b1-98e4-26ed3817ab6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:55,362] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:55,363] [INFO] Selected 28 target genomes.
[2023-03-15 13:04:55,363] [INFO] Target genome list was writen to OceanDNA-b17690/target_genomes_gtdb.txt
[2023-03-15 13:04:55,565] [INFO] Task started: fastANI
[2023-03-15 13:04:55,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgb11fb6c2-2c96-46c5-afa7-9d88b9d868d8/OceanDNA-b17690.fa --refList OceanDNA-b17690/target_genomes_gtdb.txt --output OceanDNA-b17690/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:13,310] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:13,313] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:05:13,313] [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_018672475.1	s__GCA-2724215 sp018672475	79.7094	132	189	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
GCA_015660315.1	s__GCA-2724215 sp015660315	79.194	99	189	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	77.4137	72	189	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:13,313] [INFO] GTDB search result was written to OceanDNA-b17690/result_gtdb.tsv
[2023-03-15 13:05:13,313] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:13,314] [INFO] DFAST_QC result json was written to OceanDNA-b17690/dqc_result.json
[2023-03-15 13:05:13,314] [INFO] DFAST_QC completed!
[2023-03-15 13:05:13,314] [INFO] Total running time: 0h1m18s