[2023-03-16 00:05:33,362] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:05:33,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:05:33,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference
[2023-03-16 00:05:34,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:05:34,447] [INFO] Task started: Prodigal
[2023-03-16 00:05:34,447] [INFO] Running command: cat /var/lib/cwl/stga1500f77-0490-4514-b39a-e9ec178933b9/OceanDNA-b15461.fa | prodigal -d OceanDNA-b15461/cds.fna -a OceanDNA-b15461/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:05:49,567] [INFO] Task succeeded: Prodigal
[2023-03-16 00:05:49,567] [INFO] Task started: HMMsearch
[2023-03-16 00:05:49,567] [INFO] Running command: hmmsearch --tblout OceanDNA-b15461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference/reference_markers.hmm OceanDNA-b15461/protein.faa > /dev/null
[2023-03-16 00:05:49,738] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:05:49,738] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga1500f77-0490-4514-b39a-e9ec178933b9/OceanDNA-b15461.fa]
[2023-03-16 00:05:49,771] [INFO] Query marker FASTA was written to OceanDNA-b15461/markers.fasta
[2023-03-16 00:05:49,772] [INFO] Task started: Blastn
[2023-03-16 00:05:49,772] [INFO] Running command: blastn -query OceanDNA-b15461/markers.fasta -db /var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference/reference_markers.fasta -out OceanDNA-b15461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:05:50,216] [INFO] Task succeeded: Blastn
[2023-03-16 00:05:50,222] [INFO] Selected 17 target genomes.
[2023-03-16 00:05:50,222] [INFO] Target genome list was writen to OceanDNA-b15461/target_genomes.txt
[2023-03-16 00:05:50,232] [INFO] Task started: fastANI
[2023-03-16 00:05:50,232] [INFO] Running command: fastANI --query /var/lib/cwl/stga1500f77-0490-4514-b39a-e9ec178933b9/OceanDNA-b15461.fa --refList OceanDNA-b15461/target_genomes.txt --output OceanDNA-b15461/fastani_result.tsv --threads 1
[2023-03-16 00:06:02,775] [INFO] Task succeeded: fastANI
[2023-03-16 00:06:02,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:06:02,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:06:02,776] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:06:02,776] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:06:02,776] [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 00:06:02,782] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15461/tc_result.tsv
[2023-03-16 00:06:02,790] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:06:02,790] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:06:02,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference/checkm_data
[2023-03-16 00:06:02,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:06:02,809] [INFO] Task started: CheckM
[2023-03-16 00:06:02,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15461/checkm_input OceanDNA-b15461/checkm_result
[2023-03-16 00:06:43,039] [INFO] Task succeeded: CheckM
[2023-03-16 00:06:43,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:06:43,091] [INFO] ===== Completeness check finished =====
[2023-03-16 00:06:43,092] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:06:43,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15461/markers.fasta)
[2023-03-16 00:06:43,093] [INFO] Task started: Blastn
[2023-03-16 00:06:43,093] [INFO] Running command: blastn -query OceanDNA-b15461/markers.fasta -db /var/lib/cwl/stg5a7d58ae-db96-4404-bcff-b6917a649163/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:06:43,610] [INFO] Task succeeded: Blastn
[2023-03-16 00:06:43,611] [INFO] Selected 18 target genomes.
[2023-03-16 00:06:43,611] [INFO] Target genome list was writen to OceanDNA-b15461/target_genomes_gtdb.txt
[2023-03-16 00:06:43,632] [INFO] Task started: fastANI
[2023-03-16 00:06:43,632] [INFO] Running command: fastANI --query /var/lib/cwl/stga1500f77-0490-4514-b39a-e9ec178933b9/OceanDNA-b15461.fa --refList OceanDNA-b15461/target_genomes_gtdb.txt --output OceanDNA-b15461/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:06:51,770] [INFO] Task succeeded: fastANI
[2023-03-16 00:06:51,777] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:06:51,777] [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_002816575.1	s__UBA9611 sp002816575	76.8158	108	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746355.1	s__UBA9611 sp002746355	76.6066	142	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.11	98.97	0.93	0.85	6	-
GCA_013204585.1	s__UBA9611 sp013204585	76.604	116	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721995.1	s__UBA9611 sp002721995	76.4217	137	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_002816585.1	s__UBA9611 sp002816585	76.411	96	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392095.1	s__UBA9611 sp009391975	76.2789	106	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	98.46	97.52	0.83	0.73	9	-
GCA_002730485.1	s__UBA9611 sp002730485	76.162	65	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872385.1	s__SHYG01 sp016872385	75.9529	73	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238505.1	s__Bin22 sp002238505	75.8992	54	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392075.1	s__UBA9611 sp009392075	75.7828	84	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	96.71	96.71	0.58	0.58	2	-
GCA_009840135.1	s__Bin22 sp009840135	75.6761	62	817	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:06:51,783] [INFO] GTDB search result was written to OceanDNA-b15461/result_gtdb.tsv
[2023-03-16 00:06:51,794] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:06:51,798] [INFO] DFAST_QC result json was written to OceanDNA-b15461/dqc_result.json
[2023-03-16 00:06:51,798] [INFO] DFAST_QC completed!
[2023-03-16 00:06:51,798] [INFO] Total running time: 0h1m18s