[2023-03-16 06:50:39,219] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:50:39,220] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:50:39,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference
[2023-03-16 06:50:40,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:50:40,336] [INFO] Task started: Prodigal
[2023-03-16 06:50:40,336] [INFO] Running command: cat /var/lib/cwl/stg6b6663ce-36d0-495f-8e1c-4019f5191b4a/OceanDNA-b20977.fa | prodigal -d OceanDNA-b20977/cds.fna -a OceanDNA-b20977/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:51:07,607] [INFO] Task succeeded: Prodigal
[2023-03-16 06:51:07,607] [INFO] Task started: HMMsearch
[2023-03-16 06:51:07,607] [INFO] Running command: hmmsearch --tblout OceanDNA-b20977/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference/reference_markers.hmm OceanDNA-b20977/protein.faa > /dev/null
[2023-03-16 06:51:07,844] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:51:07,845] [INFO] Found 6/6 markers.
[2023-03-16 06:51:07,875] [INFO] Query marker FASTA was written to OceanDNA-b20977/markers.fasta
[2023-03-16 06:51:07,876] [INFO] Task started: Blastn
[2023-03-16 06:51:07,876] [INFO] Running command: blastn -query OceanDNA-b20977/markers.fasta -db /var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference/reference_markers.fasta -out OceanDNA-b20977/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:51:08,417] [INFO] Task succeeded: Blastn
[2023-03-16 06:51:08,418] [INFO] Selected 36 target genomes.
[2023-03-16 06:51:08,419] [INFO] Target genome list was writen to OceanDNA-b20977/target_genomes.txt
[2023-03-16 06:51:08,439] [INFO] Task started: fastANI
[2023-03-16 06:51:08,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b6663ce-36d0-495f-8e1c-4019f5191b4a/OceanDNA-b20977.fa --refList OceanDNA-b20977/target_genomes.txt --output OceanDNA-b20977/fastani_result.tsv --threads 1
[2023-03-16 06:51:34,178] [INFO] Task succeeded: fastANI
[2023-03-16 06:51:34,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:51:34,178] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:51:34,183] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:51:34,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:51:34,183] [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
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8562	58	1442	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8553	58	1442	95	below_threshold
Corallococcus carmarthensis	strain=CA043D	GCA_003611695.1	2316728	2316728	type	True	74.7776	51	1442	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:51:34,184] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20977/tc_result.tsv
[2023-03-16 06:51:34,184] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:51:34,184] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:51:34,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference/checkm_data
[2023-03-16 06:51:34,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:51:34,300] [INFO] Task started: CheckM
[2023-03-16 06:51:34,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20977/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20977/checkm_input OceanDNA-b20977/checkm_result
[2023-03-16 06:52:40,559] [INFO] Task succeeded: CheckM
[2023-03-16 06:52:40,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:52:40,589] [INFO] ===== Completeness check finished =====
[2023-03-16 06:52:40,589] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:52:40,589] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20977/markers.fasta)
[2023-03-16 06:52:40,590] [INFO] Task started: Blastn
[2023-03-16 06:52:40,590] [INFO] Running command: blastn -query OceanDNA-b20977/markers.fasta -db /var/lib/cwl/stg7e8c5d21-210b-4784-93ed-021aac0b2ebf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20977/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:52:41,345] [INFO] Task succeeded: Blastn
[2023-03-16 06:52:41,355] [INFO] Selected 35 target genomes.
[2023-03-16 06:52:41,355] [INFO] Target genome list was writen to OceanDNA-b20977/target_genomes_gtdb.txt
[2023-03-16 06:52:41,435] [INFO] Task started: fastANI
[2023-03-16 06:52:41,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b6663ce-36d0-495f-8e1c-4019f5191b4a/OceanDNA-b20977.fa --refList OceanDNA-b20977/target_genomes_gtdb.txt --output OceanDNA-b20977/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:53:05,964] [INFO] Task succeeded: fastANI
[2023-03-16 06:53:05,967] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:53:05,967] [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_002724675.1	s__GCA-2724675 sp002724675	99.92	1325	1442	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__GCA-2724675	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002433485.1	s__UBA6601 sp002433485	76.0827	114	1442	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__UBA6601	95.0	99.91	99.91	0.95	0.95	2	-
GCA_016717595.1	s__JADKFE01 sp016717595	75.0365	60	1442	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-16 06:53:05,969] [INFO] GTDB search result was written to OceanDNA-b20977/result_gtdb.tsv
[2023-03-16 06:53:05,972] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:53:05,974] [INFO] DFAST_QC result json was written to OceanDNA-b20977/dqc_result.json
[2023-03-16 06:53:05,975] [INFO] DFAST_QC completed!
[2023-03-16 06:53:05,975] [INFO] Total running time: 0h2m27s