[2023-03-16 05:27:24,110] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:27:24,121] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:27:24,121] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference
[2023-03-16 05:27:25,201] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:27:25,201] [INFO] Task started: Prodigal
[2023-03-16 05:27:25,201] [INFO] Running command: cat /var/lib/cwl/stg720f4e16-b8a5-4d7e-914c-3aac345a2db7/OceanDNA-b16040.fa | prodigal -d OceanDNA-b16040/cds.fna -a OceanDNA-b16040/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:27:44,586] [INFO] Task succeeded: Prodigal
[2023-03-16 05:27:44,586] [INFO] Task started: HMMsearch
[2023-03-16 05:27:44,586] [INFO] Running command: hmmsearch --tblout OceanDNA-b16040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference/reference_markers.hmm OceanDNA-b16040/protein.faa > /dev/null
[2023-03-16 05:27:44,836] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:27:44,836] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg720f4e16-b8a5-4d7e-914c-3aac345a2db7/OceanDNA-b16040.fa]
[2023-03-16 05:27:44,964] [INFO] Query marker FASTA was written to OceanDNA-b16040/markers.fasta
[2023-03-16 05:27:44,966] [INFO] Task started: Blastn
[2023-03-16 05:27:44,966] [INFO] Running command: blastn -query OceanDNA-b16040/markers.fasta -db /var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference/reference_markers.fasta -out OceanDNA-b16040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:27:45,491] [INFO] Task succeeded: Blastn
[2023-03-16 05:27:45,530] [INFO] Selected 26 target genomes.
[2023-03-16 05:27:45,530] [INFO] Target genome list was writen to OceanDNA-b16040/target_genomes.txt
[2023-03-16 05:27:45,542] [INFO] Task started: fastANI
[2023-03-16 05:27:45,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg720f4e16-b8a5-4d7e-914c-3aac345a2db7/OceanDNA-b16040.fa --refList OceanDNA-b16040/target_genomes.txt --output OceanDNA-b16040/fastani_result.tsv --threads 1
[2023-03-16 05:28:07,936] [INFO] Task succeeded: fastANI
[2023-03-16 05:28:07,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:28:07,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:28:07,940] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:28:07,940] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:28:07,940] [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
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	75.1308	57	1115	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:28:07,940] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16040/tc_result.tsv
[2023-03-16 05:28:07,940] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:28:07,940] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:28:07,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference/checkm_data
[2023-03-16 05:28:07,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:28:07,948] [INFO] Task started: CheckM
[2023-03-16 05:28:07,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16040/checkm_input OceanDNA-b16040/checkm_result
[2023-03-16 05:28:58,027] [INFO] Task succeeded: CheckM
[2023-03-16 05:28:58,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 9.18%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 05:28:58,064] [INFO] ===== Completeness check finished =====
[2023-03-16 05:28:58,064] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:28:58,065] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16040/markers.fasta)
[2023-03-16 05:28:58,066] [INFO] Task started: Blastn
[2023-03-16 05:28:58,066] [INFO] Running command: blastn -query OceanDNA-b16040/markers.fasta -db /var/lib/cwl/stg7ec15ba4-1c19-4db5-85c4-f2541d84d04b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:28:58,768] [INFO] Task succeeded: Blastn
[2023-03-16 05:28:58,769] [INFO] Selected 31 target genomes.
[2023-03-16 05:28:58,769] [INFO] Target genome list was writen to OceanDNA-b16040/target_genomes_gtdb.txt
[2023-03-16 05:28:58,795] [INFO] Task started: fastANI
[2023-03-16 05:28:58,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg720f4e16-b8a5-4d7e-914c-3aac345a2db7/OceanDNA-b16040.fa --refList OceanDNA-b16040/target_genomes_gtdb.txt --output OceanDNA-b16040/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:29:27,386] [INFO] Task succeeded: fastANI
[2023-03-16 05:29:27,390] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:29:27,391] [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_001890975.1	s__Roseofilum reptotaenium_A	77.1884	300	1115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Roseofilum	95.0	97.72	97.70	0.90	0.89	3	-
GCA_002340255.1	s__Roseofilum sp002340255	77.1093	278	1115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Roseofilum	95.0	99.04	97.93	0.93	0.88	11	-
GCF_001746915.1	s__Desertifilum sp001746915	75.5329	82	1115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Desertifilaceae;g__Desertifilum	95.0	99.94	99.93	0.99	0.98	4	-
GCA_015295945.1	s__DVED01 sp003695795	75.4958	59	1115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__DVED01	95.0	99.89	99.88	0.96	0.93	3	-
GCF_012295525.1	s__Oxynema aestuarii	75.3445	59	1115	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oxynema	95.0	97.71	95.88	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 05:29:27,400] [INFO] GTDB search result was written to OceanDNA-b16040/result_gtdb.tsv
[2023-03-16 05:29:27,404] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:29:27,404] [INFO] DFAST_QC result json was written to OceanDNA-b16040/dqc_result.json
[2023-03-16 05:29:27,404] [INFO] DFAST_QC completed!
[2023-03-16 05:29:27,405] [INFO] Total running time: 0h2m3s