[2023-03-15 14:37:46,931] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:46,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:46,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference
[2023-03-15 14:37:48,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:48,675] [INFO] Task started: Prodigal
[2023-03-15 14:37:48,675] [INFO] Running command: cat /var/lib/cwl/stgcdc41fa5-01a6-478a-8787-fe4fa506d07a/OceanDNA-b22885.fa | prodigal -d OceanDNA-b22885/cds.fna -a OceanDNA-b22885/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:43,707] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:43,708] [INFO] Task started: HMMsearch
[2023-03-15 14:38:43,708] [INFO] Running command: hmmsearch --tblout OceanDNA-b22885/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference/reference_markers.hmm OceanDNA-b22885/protein.faa > /dev/null
[2023-03-15 14:38:44,052] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:44,052] [INFO] Found 6/6 markers.
[2023-03-15 14:38:44,105] [INFO] Query marker FASTA was written to OceanDNA-b22885/markers.fasta
[2023-03-15 14:38:44,106] [INFO] Task started: Blastn
[2023-03-15 14:38:44,106] [INFO] Running command: blastn -query OceanDNA-b22885/markers.fasta -db /var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference/reference_markers.fasta -out OceanDNA-b22885/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:44,627] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:44,628] [INFO] Selected 16 target genomes.
[2023-03-15 14:38:44,628] [INFO] Target genome list was writen to OceanDNA-b22885/target_genomes.txt
[2023-03-15 14:38:44,639] [INFO] Task started: fastANI
[2023-03-15 14:38:44,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdc41fa5-01a6-478a-8787-fe4fa506d07a/OceanDNA-b22885.fa --refList OceanDNA-b22885/target_genomes.txt --output OceanDNA-b22885/fastani_result.tsv --threads 1
[2023-03-15 14:38:58,963] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:58,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:58,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:58,967] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:58,968] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:38:58,968] [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
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	76.7891	210	2797	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	74.9661	50	2797	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:38:58,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22885/tc_result.tsv
[2023-03-15 14:38:58,968] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:58,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:58,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference/checkm_data
[2023-03-15 14:38:58,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:58,979] [INFO] Task started: CheckM
[2023-03-15 14:38:58,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22885/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22885/checkm_input OceanDNA-b22885/checkm_result
[2023-03-15 14:41:06,827] [INFO] Task succeeded: CheckM
[2023-03-15 14:41:06,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:41:06,868] [INFO] ===== Completeness check finished =====
[2023-03-15 14:41:06,868] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:41:06,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22885/markers.fasta)
[2023-03-15 14:41:06,869] [INFO] Task started: Blastn
[2023-03-15 14:41:06,870] [INFO] Running command: blastn -query OceanDNA-b22885/markers.fasta -db /var/lib/cwl/stg7581a4cd-7304-490a-9ce5-3ca81febe1ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22885/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:41:07,598] [INFO] Task succeeded: Blastn
[2023-03-15 14:41:07,599] [INFO] Selected 22 target genomes.
[2023-03-15 14:41:07,599] [INFO] Target genome list was writen to OceanDNA-b22885/target_genomes_gtdb.txt
[2023-03-15 14:41:07,652] [INFO] Task started: fastANI
[2023-03-15 14:41:07,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdc41fa5-01a6-478a-8787-fe4fa506d07a/OceanDNA-b22885.fa --refList OceanDNA-b22885/target_genomes_gtdb.txt --output OceanDNA-b22885/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:41:23,548] [INFO] Task succeeded: fastANI
[2023-03-15 14:41:23,552] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:41:23,552] [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_001983935.1	s__Fuerstia marisgermanicae	76.7667	212	2797	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238335.1	s__Fuerstia sp014238335	75.9233	166	2797	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485495.1	s__S139-18 sp015485495	75.3219	50	2797	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__S139-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924405.1	s__SXXK01 sp903924405	75.121	58	2797	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.71	99.71	0.88	0.88	2	-
GCA_016795145.1	s__SXXK01 sp016795145	75.1182	82	2797	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:41:23,552] [INFO] GTDB search result was written to OceanDNA-b22885/result_gtdb.tsv
[2023-03-15 14:41:23,553] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:41:23,554] [INFO] DFAST_QC result json was written to OceanDNA-b22885/dqc_result.json
[2023-03-15 14:41:23,555] [INFO] DFAST_QC completed!
[2023-03-15 14:41:23,555] [INFO] Total running time: 0h3m37s