[2023-03-16 23:05:03,847] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference
[2023-03-16 23:05:05,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stg8b395b25-befd-4a22-afb2-b6eae7df61c1/OceanDNA-b16785.fa | prodigal -d OceanDNA-b16785/cds.fna -a OceanDNA-b16785/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:18,367] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:18,368] [INFO] Task started: HMMsearch
[2023-03-16 23:05:18,368] [INFO] Running command: hmmsearch --tblout OceanDNA-b16785/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference/reference_markers.hmm OceanDNA-b16785/protein.faa > /dev/null
[2023-03-16 23:05:18,601] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:18,601] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b395b25-befd-4a22-afb2-b6eae7df61c1/OceanDNA-b16785.fa]
[2023-03-16 23:05:18,628] [INFO] Query marker FASTA was written to OceanDNA-b16785/markers.fasta
[2023-03-16 23:05:18,628] [INFO] Task started: Blastn
[2023-03-16 23:05:18,628] [INFO] Running command: blastn -query OceanDNA-b16785/markers.fasta -db /var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference/reference_markers.fasta -out OceanDNA-b16785/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:19,127] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:19,128] [INFO] Selected 15 target genomes.
[2023-03-16 23:05:19,128] [INFO] Target genome list was writen to OceanDNA-b16785/target_genomes.txt
[2023-03-16 23:05:19,136] [INFO] Task started: fastANI
[2023-03-16 23:05:19,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b395b25-befd-4a22-afb2-b6eae7df61c1/OceanDNA-b16785.fa --refList OceanDNA-b16785/target_genomes.txt --output OceanDNA-b16785/fastani_result.tsv --threads 1
[2023-03-16 23:05:30,232] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:30,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:30,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:30,232] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:30,232] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:05:30,232] [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
--------------------------------------------------------------------------------
[2023-03-16 23:05:30,233] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16785/tc_result.tsv
[2023-03-16 23:05:30,233] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:30,233] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:30,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference/checkm_data
[2023-03-16 23:05:30,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:30,241] [INFO] Task started: CheckM
[2023-03-16 23:05:30,241] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16785/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16785/checkm_input OceanDNA-b16785/checkm_result
[2023-03-16 23:06:07,631] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:07,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.70%
Contamintation: 2.78%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-03-16 23:06:07,634] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:07,634] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:07,634] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16785/markers.fasta)
[2023-03-16 23:06:07,635] [INFO] Task started: Blastn
[2023-03-16 23:06:07,635] [INFO] Running command: blastn -query OceanDNA-b16785/markers.fasta -db /var/lib/cwl/stg764444f7-cf6e-4f5f-93f9-9b7f1eb1892f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16785/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:08,306] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:08,307] [INFO] Selected 16 target genomes.
[2023-03-16 23:06:08,307] [INFO] Target genome list was writen to OceanDNA-b16785/target_genomes_gtdb.txt
[2023-03-16 23:06:08,823] [INFO] Task started: fastANI
[2023-03-16 23:06:08,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b395b25-befd-4a22-afb2-b6eae7df61c1/OceanDNA-b16785.fa --refList OceanDNA-b16785/target_genomes_gtdb.txt --output OceanDNA-b16785/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:21,696] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:21,700] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:21,700] [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_016212515.1	s__Obscuribacter sp016212515	77.951	108	594	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__Obscuribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712465.1	s__Obscuribacter sp016712465	77.9063	143	594	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__Obscuribacter	95.0	98.79	98.15	0.95	0.94	3	-
GCA_001899315.1	s__Obscuribacter phosphatis	77.8375	91	594	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__Obscuribacter	95.0	97.98	95.26	0.96	0.92	5	-
GCA_016718315.1	s__Obscuribacter sp016718315	77.4534	107	594	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__Obscuribacter	95.0	98.48	97.88	0.93	0.91	9	-
GCA_018266215.1	s__REEB67 sp018266215	76.848	67	594	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Obscuribacterales;f__Obscuribacteraceae;g__REEB67	95.0	97.38	97.38	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:21,700] [INFO] GTDB search result was written to OceanDNA-b16785/result_gtdb.tsv
[2023-03-16 23:06:21,700] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:21,701] [INFO] DFAST_QC result json was written to OceanDNA-b16785/dqc_result.json
[2023-03-16 23:06:21,701] [INFO] DFAST_QC completed!
[2023-03-16 23:06:21,701] [INFO] Total running time: 0h1m18s