[2023-03-19 04:11:06,930] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,930] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference
[2023-03-19 04:11:08,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,645] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,645] [INFO] Running command: cat /var/lib/cwl/stg78e1af4d-1525-4786-a1db-4d7572f9db1f/OceanDNA-b30837.fa | prodigal -d OceanDNA-b30837/cds.fna -a OceanDNA-b30837/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:17,384] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:17,384] [INFO] Task started: HMMsearch
[2023-03-19 04:11:17,384] [INFO] Running command: hmmsearch --tblout OceanDNA-b30837/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference/reference_markers.hmm OceanDNA-b30837/protein.faa > /dev/null
[2023-03-19 04:11:17,559] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:17,559] [INFO] Found 6/6 markers.
[2023-03-19 04:11:17,576] [INFO] Query marker FASTA was written to OceanDNA-b30837/markers.fasta
[2023-03-19 04:11:17,576] [INFO] Task started: Blastn
[2023-03-19 04:11:17,576] [INFO] Running command: blastn -query OceanDNA-b30837/markers.fasta -db /var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference/reference_markers.fasta -out OceanDNA-b30837/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:18,179] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:18,180] [INFO] Selected 29 target genomes.
[2023-03-19 04:11:18,180] [INFO] Target genome list was writen to OceanDNA-b30837/target_genomes.txt
[2023-03-19 04:11:18,200] [INFO] Task started: fastANI
[2023-03-19 04:11:18,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e1af4d-1525-4786-a1db-4d7572f9db1f/OceanDNA-b30837.fa --refList OceanDNA-b30837/target_genomes.txt --output OceanDNA-b30837/fastani_result.tsv --threads 1
[2023-03-19 04:11:37,845] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:37,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:37,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:37,846] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:37,846] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:37,846] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:37,846] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30837/tc_result.tsv
[2023-03-19 04:11:37,846] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:37,846] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:37,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference/checkm_data
[2023-03-19 04:11:37,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:37,853] [INFO] Task started: CheckM
[2023-03-19 04:11:37,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30837/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30837/checkm_input OceanDNA-b30837/checkm_result
[2023-03-19 04:12:04,864] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:04,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.10%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:04,867] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:04,867] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:04,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30837/markers.fasta)
[2023-03-19 04:12:04,867] [INFO] Task started: Blastn
[2023-03-19 04:12:04,867] [INFO] Running command: blastn -query OceanDNA-b30837/markers.fasta -db /var/lib/cwl/stg09fe0d7d-61fc-4467-9fb6-2ee1d8119b3a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30837/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:05,863] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:05,864] [INFO] Selected 25 target genomes.
[2023-03-19 04:12:05,864] [INFO] Target genome list was writen to OceanDNA-b30837/target_genomes_gtdb.txt
[2023-03-19 04:12:06,120] [INFO] Task started: fastANI
[2023-03-19 04:12:06,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e1af4d-1525-4786-a1db-4d7572f9db1f/OceanDNA-b30837.fa --refList OceanDNA-b30837/target_genomes_gtdb.txt --output OceanDNA-b30837/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:20,470] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:20,473] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:12:20,473] [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_002938045.1	s__PTLJ01 sp002938045	97.5205	276	435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__PTLJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016187325.1	s__JACPJY01 sp016187325	76.8377	58	435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.6554	70	435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.5643	58	435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:20,474] [INFO] GTDB search result was written to OceanDNA-b30837/result_gtdb.tsv
[2023-03-19 04:12:20,474] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:20,474] [INFO] DFAST_QC result json was written to OceanDNA-b30837/dqc_result.json
[2023-03-19 04:12:20,474] [INFO] DFAST_QC completed!
[2023-03-19 04:12:20,475] [INFO] Total running time: 0h1m14s