[2023-03-18 00:05:54,513] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference
[2023-03-18 00:05:55,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,746] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,746] [INFO] Running command: cat /var/lib/cwl/stgc1a46585-72dd-40c9-95f7-f0fa615ceee8/OceanDNA-b187.fa | prodigal -d OceanDNA-b187/cds.fna -a OceanDNA-b187/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:10,950] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:10,951] [INFO] Task started: HMMsearch
[2023-03-18 00:06:10,951] [INFO] Running command: hmmsearch --tblout OceanDNA-b187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference/reference_markers.hmm OceanDNA-b187/protein.faa > /dev/null
[2023-03-18 00:06:11,128] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:11,129] [INFO] Found 6/6 markers.
[2023-03-18 00:06:11,145] [INFO] Query marker FASTA was written to OceanDNA-b187/markers.fasta
[2023-03-18 00:06:11,146] [INFO] Task started: Blastn
[2023-03-18 00:06:11,146] [INFO] Running command: blastn -query OceanDNA-b187/markers.fasta -db /var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference/reference_markers.fasta -out OceanDNA-b187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:11,684] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:11,684] [INFO] Selected 25 target genomes.
[2023-03-18 00:06:11,685] [INFO] Target genome list was writen to OceanDNA-b187/target_genomes.txt
[2023-03-18 00:06:11,699] [INFO] Task started: fastANI
[2023-03-18 00:06:11,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1a46585-72dd-40c9-95f7-f0fa615ceee8/OceanDNA-b187.fa --refList OceanDNA-b187/target_genomes.txt --output OceanDNA-b187/fastani_result.tsv --threads 1
[2023-03-18 00:06:30,601] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:30,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:30,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:30,602] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:30,602] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:06:30,602] [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 00:06:30,603] [INFO] DFAST Taxonomy check result was written to OceanDNA-b187/tc_result.tsv
[2023-03-18 00:06:30,609] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:30,609] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:30,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference/checkm_data
[2023-03-18 00:06:30,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:30,618] [INFO] Task started: CheckM
[2023-03-18 00:06:30,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b187/checkm_input OceanDNA-b187/checkm_result
[2023-03-18 00:07:10,963] [INFO] Task succeeded: CheckM
[2023-03-18 00:07:10,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:07:11,024] [INFO] ===== Completeness check finished =====
[2023-03-18 00:07:11,025] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:07:11,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b187/markers.fasta)
[2023-03-18 00:07:11,026] [INFO] Task started: Blastn
[2023-03-18 00:07:11,026] [INFO] Running command: blastn -query OceanDNA-b187/markers.fasta -db /var/lib/cwl/stg3028bebf-be1e-4d01-9707-7056339df52b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:07:11,769] [INFO] Task succeeded: Blastn
[2023-03-18 00:07:11,772] [INFO] Selected 22 target genomes.
[2023-03-18 00:07:11,772] [INFO] Target genome list was writen to OceanDNA-b187/target_genomes_gtdb.txt
[2023-03-18 00:07:11,783] [INFO] Task started: fastANI
[2023-03-18 00:07:11,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1a46585-72dd-40c9-95f7-f0fa615ceee8/OceanDNA-b187.fa --refList OceanDNA-b187/target_genomes_gtdb.txt --output OceanDNA-b187/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:07:23,828] [INFO] Task succeeded: fastANI
[2023-03-18 00:07:23,833] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:07:23,833] [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_002296225.1	s__UBA823 sp002296225	99.1526	714	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA823	95.0	99.57	99.38	0.83	0.81	4	conclusive
GCA_002730735.1	s__UBA11600 sp002730735	79.6344	173	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717745.1	s__UBA11600 sp002717745	78.894	161	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714165.1	s__UBA11600 sp002714165	78.6342	205	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA11600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730525.1	s__UBA2161 sp002730525	76.9333	214	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328835.1	s__UBA2161 sp002328835	76.8903	233	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA2161	95.0	99.85	99.81	0.96	0.95	4	-
GCA_011523845.1	s__WTFV01 sp011523845	75.5585	60	826	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA8438;g__WTFV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:07:23,837] [INFO] GTDB search result was written to OceanDNA-b187/result_gtdb.tsv
[2023-03-18 00:07:23,839] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:07:23,840] [INFO] DFAST_QC result json was written to OceanDNA-b187/dqc_result.json
[2023-03-18 00:07:23,840] [INFO] DFAST_QC completed!
[2023-03-18 00:07:23,840] [INFO] Total running time: 0h1m29s