[2023-03-17 04:48:54,029] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference
[2023-03-17 04:48:55,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,306] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,306] [INFO] Running command: cat /var/lib/cwl/stgf0989190-14fc-4535-bc51-134902a934fe/OceanDNA-b11534.fa | prodigal -d OceanDNA-b11534/cds.fna -a OceanDNA-b11534/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:06,901] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:06,902] [INFO] Task started: HMMsearch
[2023-03-17 04:49:06,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b11534/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference/reference_markers.hmm OceanDNA-b11534/protein.faa > /dev/null
[2023-03-17 04:49:07,079] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:07,079] [INFO] Found 6/6 markers.
[2023-03-17 04:49:07,093] [INFO] Query marker FASTA was written to OceanDNA-b11534/markers.fasta
[2023-03-17 04:49:07,093] [INFO] Task started: Blastn
[2023-03-17 04:49:07,093] [INFO] Running command: blastn -query OceanDNA-b11534/markers.fasta -db /var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference/reference_markers.fasta -out OceanDNA-b11534/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:07,609] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:07,609] [INFO] Selected 20 target genomes.
[2023-03-17 04:49:07,610] [INFO] Target genome list was writen to OceanDNA-b11534/target_genomes.txt
[2023-03-17 04:49:07,620] [INFO] Task started: fastANI
[2023-03-17 04:49:07,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0989190-14fc-4535-bc51-134902a934fe/OceanDNA-b11534.fa --refList OceanDNA-b11534/target_genomes.txt --output OceanDNA-b11534/fastani_result.tsv --threads 1
[2023-03-17 04:49:20,438] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:20,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:20,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:20,439] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:20,439] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:20,439] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:20,439] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11534/tc_result.tsv
[2023-03-17 04:49:20,439] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:20,439] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:20,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference/checkm_data
[2023-03-17 04:49:20,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:20,445] [INFO] Task started: CheckM
[2023-03-17 04:49:20,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11534/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11534/checkm_input OceanDNA-b11534/checkm_result
[2023-03-17 04:49:54,649] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:54,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:54,651] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:54,651] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:54,652] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11534/markers.fasta)
[2023-03-17 04:49:54,653] [INFO] Task started: Blastn
[2023-03-17 04:49:54,653] [INFO] Running command: blastn -query OceanDNA-b11534/markers.fasta -db /var/lib/cwl/stg0a6c91a0-fb56-43ce-9cbb-60349a2c66c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11534/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:55,354] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:55,355] [INFO] Selected 27 target genomes.
[2023-03-17 04:49:55,355] [INFO] Target genome list was writen to OceanDNA-b11534/target_genomes_gtdb.txt
[2023-03-17 04:49:56,235] [INFO] Task started: fastANI
[2023-03-17 04:49:56,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0989190-14fc-4535-bc51-134902a934fe/OceanDNA-b11534.fa --refList OceanDNA-b11534/target_genomes_gtdb.txt --output OceanDNA-b11534/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:09,054] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:09,057] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:50:09,058] [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_012965955.1	s__GCA-2400975 sp012965955	97.6256	331	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__NORP154;g__GCA-2400975	95.0	99.35	99.35	0.74	0.74	2	conclusive
GCA_016764395.1	s__GCA-2400975 sp016764395	77.026	70	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__NORP154;g__GCA-2400975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400975.1	s__GCA-2400975 sp002400975	76.33	51	413	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__NORP154;g__GCA-2400975	95.0	96.86	96.86	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:09,058] [INFO] GTDB search result was written to OceanDNA-b11534/result_gtdb.tsv
[2023-03-17 04:50:09,058] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:09,058] [INFO] DFAST_QC result json was written to OceanDNA-b11534/dqc_result.json
[2023-03-17 04:50:09,058] [INFO] DFAST_QC completed!
[2023-03-17 04:50:09,058] [INFO] Total running time: 0h1m15s