[2023-03-18 00:05:54,410] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,410] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference
[2023-03-18 00:05:55,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,566] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,567] [INFO] Running command: cat /var/lib/cwl/stgf55a32ed-dbba-4cd2-b1e8-35a4c2b574e7/OceanDNA-b7089.fa | prodigal -d OceanDNA-b7089/cds.fna -a OceanDNA-b7089/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:05:59,993] [INFO] Task succeeded: Prodigal
[2023-03-18 00:05:59,993] [INFO] Task started: HMMsearch
[2023-03-18 00:05:59,993] [INFO] Running command: hmmsearch --tblout OceanDNA-b7089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference/reference_markers.hmm OceanDNA-b7089/protein.faa > /dev/null
[2023-03-18 00:06:00,181] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:00,182] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf55a32ed-dbba-4cd2-b1e8-35a4c2b574e7/OceanDNA-b7089.fa]
[2023-03-18 00:06:00,190] [INFO] Query marker FASTA was written to OceanDNA-b7089/markers.fasta
[2023-03-18 00:06:00,191] [INFO] Task started: Blastn
[2023-03-18 00:06:00,191] [INFO] Running command: blastn -query OceanDNA-b7089/markers.fasta -db /var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference/reference_markers.fasta -out OceanDNA-b7089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:00,742] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:00,743] [INFO] Selected 28 target genomes.
[2023-03-18 00:06:00,743] [INFO] Target genome list was writen to OceanDNA-b7089/target_genomes.txt
[2023-03-18 00:06:00,760] [INFO] Task started: fastANI
[2023-03-18 00:06:00,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55a32ed-dbba-4cd2-b1e8-35a4c2b574e7/OceanDNA-b7089.fa --refList OceanDNA-b7089/target_genomes.txt --output OceanDNA-b7089/fastani_result.tsv --threads 1
[2023-03-18 00:06:17,517] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:17,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:17,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:17,517] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:17,517] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:06:17,518] [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
--------------------------------------------------------------------------------
[2023-03-18 00:06:17,518] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7089/tc_result.tsv
[2023-03-18 00:06:17,518] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:17,518] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:17,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference/checkm_data
[2023-03-18 00:06:17,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:17,566] [INFO] Task started: CheckM
[2023-03-18 00:06:17,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7089/checkm_input OceanDNA-b7089/checkm_result
[2023-03-18 00:06:35,158] [INFO] Task succeeded: CheckM
[2023-03-18 00:06:35,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:06:35,175] [INFO] ===== Completeness check finished =====
[2023-03-18 00:06:35,175] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:06:35,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7089/markers.fasta)
[2023-03-18 00:06:35,177] [INFO] Task started: Blastn
[2023-03-18 00:06:35,177] [INFO] Running command: blastn -query OceanDNA-b7089/markers.fasta -db /var/lib/cwl/stg6f07cb00-6ec7-4edb-8a14-799843f71466/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:36,027] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:36,028] [INFO] Selected 15 target genomes.
[2023-03-18 00:06:36,028] [INFO] Target genome list was writen to OceanDNA-b7089/target_genomes_gtdb.txt
[2023-03-18 00:06:36,043] [INFO] Task started: fastANI
[2023-03-18 00:06:36,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55a32ed-dbba-4cd2-b1e8-35a4c2b574e7/OceanDNA-b7089.fa --refList OceanDNA-b7089/target_genomes_gtdb.txt --output OceanDNA-b7089/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:06:39,349] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:39,353] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:06:39,354] [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_014239895.1	s__GCA-2700405 sp014239895	97.1303	154	206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018657955.1	s__GCA-2700405 sp018657955	91.0199	194	206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	-
GCA_902512065.1	s__GCA-2700405 sp902512065	83.0484	141	206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213965.1	s__GCA-2700405 sp004213965	82.6227	147	206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700405.1	s__GCA-2700405 sp002700405	81.6104	150	206	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:06:39,355] [INFO] GTDB search result was written to OceanDNA-b7089/result_gtdb.tsv
[2023-03-18 00:06:39,356] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:06:39,358] [INFO] DFAST_QC result json was written to OceanDNA-b7089/dqc_result.json
[2023-03-18 00:06:39,358] [INFO] DFAST_QC completed!
[2023-03-18 00:06:39,358] [INFO] Total running time: 0h0m45s