[2023-03-18 09:41:09,194] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:09,194] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:09,194] [INFO] DQC Reference Directory: /var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference
[2023-03-18 09:41:10,341] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:10,341] [INFO] Task started: Prodigal
[2023-03-18 09:41:10,341] [INFO] Running command: cat /var/lib/cwl/stg2ebac627-fc02-43ac-8757-a948e419436c/OceanDNA-b41323.fa | prodigal -d OceanDNA-b41323/cds.fna -a OceanDNA-b41323/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:26,586] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:26,586] [INFO] Task started: HMMsearch
[2023-03-18 09:41:26,586] [INFO] Running command: hmmsearch --tblout OceanDNA-b41323/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference/reference_markers.hmm OceanDNA-b41323/protein.faa > /dev/null
[2023-03-18 09:41:26,816] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:26,817] [INFO] Found 6/6 markers.
[2023-03-18 09:41:26,841] [INFO] Query marker FASTA was written to OceanDNA-b41323/markers.fasta
[2023-03-18 09:41:26,841] [INFO] Task started: Blastn
[2023-03-18 09:41:26,841] [INFO] Running command: blastn -query OceanDNA-b41323/markers.fasta -db /var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference/reference_markers.fasta -out OceanDNA-b41323/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:27,394] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:27,394] [INFO] Selected 33 target genomes.
[2023-03-18 09:41:27,395] [INFO] Target genome list was writen to OceanDNA-b41323/target_genomes.txt
[2023-03-18 09:41:27,415] [INFO] Task started: fastANI
[2023-03-18 09:41:27,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebac627-fc02-43ac-8757-a948e419436c/OceanDNA-b41323.fa --refList OceanDNA-b41323/target_genomes.txt --output OceanDNA-b41323/fastani_result.tsv --threads 1
[2023-03-18 09:41:50,663] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:50,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:50,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:50,667] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:50,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:41:50,668] [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
Bermanella marisrubri	strain=RED65	GCA_012295615.1	207949	207949	type	True	77.3689	138	939	95	below_threshold
Bermanella marisrubri	strain=RED65	GCA_000153565.1	207949	207949	type	True	77.2465	138	939	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:41:50,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41323/tc_result.tsv
[2023-03-18 09:41:50,669] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:50,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:50,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference/checkm_data
[2023-03-18 09:41:50,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:50,675] [INFO] Task started: CheckM
[2023-03-18 09:41:50,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41323/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41323/checkm_input OceanDNA-b41323/checkm_result
[2023-03-18 09:42:34,040] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:34,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:34,042] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:34,043] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:34,043] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41323/markers.fasta)
[2023-03-18 09:42:34,043] [INFO] Task started: Blastn
[2023-03-18 09:42:34,043] [INFO] Running command: blastn -query OceanDNA-b41323/markers.fasta -db /var/lib/cwl/stgbabec54d-1428-4602-81e5-f6cd6af34e84/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41323/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:34,797] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:34,798] [INFO] Selected 23 target genomes.
[2023-03-18 09:42:34,798] [INFO] Target genome list was writen to OceanDNA-b41323/target_genomes_gtdb.txt
[2023-03-18 09:42:34,814] [INFO] Task started: fastANI
[2023-03-18 09:42:34,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebac627-fc02-43ac-8757-a948e419436c/OceanDNA-b41323.fa --refList OceanDNA-b41323/target_genomes_gtdb.txt --output OceanDNA-b41323/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:49,024] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:49,028] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:42:49,029] [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_002683575.1	s__Bermanella sp002683575	99.6289	814	939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.58	99.58	0.89	0.89	2	conclusive
GCA_013373125.1	s__Bermanella sp013373125	79.4921	456	939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012295615.1	s__Bermanella marisrubri	77.3689	138	939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002162985.1	s__Bermanella sp002162985	77.0426	112	939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Bermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000967895.1	s__Oleispira antarctica	76.2596	57	939	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleispira	95.0	99.07	99.06	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:49,029] [INFO] GTDB search result was written to OceanDNA-b41323/result_gtdb.tsv
[2023-03-18 09:42:49,029] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:49,030] [INFO] DFAST_QC result json was written to OceanDNA-b41323/dqc_result.json
[2023-03-18 09:42:49,030] [INFO] DFAST_QC completed!
[2023-03-18 09:42:49,030] [INFO] Total running time: 0h1m40s