[2023-03-18 08:17:20,561] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference
[2023-03-18 08:17:21,703] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,703] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,704] [INFO] Running command: cat /var/lib/cwl/stg59ec05a4-07db-432f-a346-df37ddbc52cc/OceanDNA-b30499.fa | prodigal -d OceanDNA-b30499/cds.fna -a OceanDNA-b30499/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:30,507] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:30,507] [INFO] Task started: HMMsearch
[2023-03-18 08:17:30,507] [INFO] Running command: hmmsearch --tblout OceanDNA-b30499/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference/reference_markers.hmm OceanDNA-b30499/protein.faa > /dev/null
[2023-03-18 08:17:30,715] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:30,715] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg59ec05a4-07db-432f-a346-df37ddbc52cc/OceanDNA-b30499.fa]
[2023-03-18 08:17:30,730] [INFO] Query marker FASTA was written to OceanDNA-b30499/markers.fasta
[2023-03-18 08:17:30,731] [INFO] Task started: Blastn
[2023-03-18 08:17:30,731] [INFO] Running command: blastn -query OceanDNA-b30499/markers.fasta -db /var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference/reference_markers.fasta -out OceanDNA-b30499/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:31,373] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:31,374] [INFO] Selected 30 target genomes.
[2023-03-18 08:17:31,374] [INFO] Target genome list was writen to OceanDNA-b30499/target_genomes.txt
[2023-03-18 08:17:31,397] [INFO] Task started: fastANI
[2023-03-18 08:17:31,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ec05a4-07db-432f-a346-df37ddbc52cc/OceanDNA-b30499.fa --refList OceanDNA-b30499/target_genomes.txt --output OceanDNA-b30499/fastani_result.tsv --threads 1
[2023-03-18 08:17:49,754] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:49,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:49,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:49,759] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:49,759] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:49,759] [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
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	76.7413	60	418	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.4658	51	418	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.1582	54	418	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.1323	55	418	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:49,759] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30499/tc_result.tsv
[2023-03-18 08:17:49,759] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:49,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:49,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference/checkm_data
[2023-03-18 08:17:49,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:49,763] [INFO] Task started: CheckM
[2023-03-18 08:17:49,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30499/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30499/checkm_input OceanDNA-b30499/checkm_result
[2023-03-18 08:18:17,043] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:17,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.72%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:17,046] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:17,046] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:17,046] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30499/markers.fasta)
[2023-03-18 08:18:17,047] [INFO] Task started: Blastn
[2023-03-18 08:18:17,047] [INFO] Running command: blastn -query OceanDNA-b30499/markers.fasta -db /var/lib/cwl/stg1361bad9-05fb-4fe6-9b07-465a4b5086a5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30499/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:18,134] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:18,135] [INFO] Selected 29 target genomes.
[2023-03-18 08:18:18,135] [INFO] Target genome list was writen to OceanDNA-b30499/target_genomes_gtdb.txt
[2023-03-18 08:18:18,274] [INFO] Task started: fastANI
[2023-03-18 08:18:18,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ec05a4-07db-432f-a346-df37ddbc52cc/OceanDNA-b30499.fa --refList OceanDNA-b30499/target_genomes_gtdb.txt --output OceanDNA-b30499/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:35,305] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:35,308] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:18:35,309] [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
GCF_000152625.1	s__Roseovarius nubinhibens	76.7413	60	418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_900143535.1	s__Tateyamaria sp900143535	76.0583	52	418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	75.9217	51	418	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:35,309] [INFO] GTDB search result was written to OceanDNA-b30499/result_gtdb.tsv
[2023-03-18 08:18:35,309] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:35,310] [INFO] DFAST_QC result json was written to OceanDNA-b30499/dqc_result.json
[2023-03-18 08:18:35,310] [INFO] DFAST_QC completed!
[2023-03-18 08:18:35,310] [INFO] Total running time: 0h1m15s