[2023-03-18 08:31:56,342] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,342] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,342] [INFO] DQC Reference Directory: /var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference
[2023-03-18 08:31:57,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,438] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,439] [INFO] Running command: cat /var/lib/cwl/stg48e794e2-c676-4ad2-9dfe-97165e477484/OceanDNA-b4197.fa | prodigal -d OceanDNA-b4197/cds.fna -a OceanDNA-b4197/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:19,889] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:19,890] [INFO] Task started: HMMsearch
[2023-03-18 08:32:19,890] [INFO] Running command: hmmsearch --tblout OceanDNA-b4197/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference/reference_markers.hmm OceanDNA-b4197/protein.faa > /dev/null
[2023-03-18 08:32:20,088] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:20,089] [INFO] Found 6/6 markers.
[2023-03-18 08:32:20,110] [INFO] Query marker FASTA was written to OceanDNA-b4197/markers.fasta
[2023-03-18 08:32:20,111] [INFO] Task started: Blastn
[2023-03-18 08:32:20,111] [INFO] Running command: blastn -query OceanDNA-b4197/markers.fasta -db /var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference/reference_markers.fasta -out OceanDNA-b4197/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:20,623] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:20,623] [INFO] Selected 29 target genomes.
[2023-03-18 08:32:20,624] [INFO] Target genome list was writen to OceanDNA-b4197/target_genomes.txt
[2023-03-18 08:32:20,638] [INFO] Task started: fastANI
[2023-03-18 08:32:20,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e794e2-c676-4ad2-9dfe-97165e477484/OceanDNA-b4197.fa --refList OceanDNA-b4197/target_genomes.txt --output OceanDNA-b4197/fastani_result.tsv --threads 1
[2023-03-18 08:32:42,584] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:42,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:42,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:42,585] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:42,585] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:32:42,585] [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 08:32:42,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4197/tc_result.tsv
[2023-03-18 08:32:42,936] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:42,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:42,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference/checkm_data
[2023-03-18 08:32:42,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:42,995] [INFO] Task started: CheckM
[2023-03-18 08:32:42,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4197/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4197/checkm_input OceanDNA-b4197/checkm_result
[2023-03-18 08:33:41,196] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:41,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:41,199] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:41,199] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:41,199] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4197/markers.fasta)
[2023-03-18 08:33:41,200] [INFO] Task started: Blastn
[2023-03-18 08:33:41,200] [INFO] Running command: blastn -query OceanDNA-b4197/markers.fasta -db /var/lib/cwl/stge0b5cee5-bcf9-4e44-9470-0501ab119daf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4197/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:41,878] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:41,879] [INFO] Selected 8 target genomes.
[2023-03-18 08:33:41,879] [INFO] Target genome list was writen to OceanDNA-b4197/target_genomes_gtdb.txt
[2023-03-18 08:33:41,897] [INFO] Task started: fastANI
[2023-03-18 08:33:41,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg48e794e2-c676-4ad2-9dfe-97165e477484/OceanDNA-b4197.fa --refList OceanDNA-b4197/target_genomes_gtdb.txt --output OceanDNA-b4197/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:46,855] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:46,859] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:33:46,859] [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_002292365.1	s__UBA4465 sp002292365	99.7393	793	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.58	99.58	0.82	0.82	2	conclusive
GCA_905182375.1	s__UBA4465 sp905182375	93.5107	752	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479015.1	s__UBA4465 sp002470835	92.7865	819	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.62	98.40	0.95	0.92	11	-
GCA_905182655.1	s__UBA4465 sp905182655	86.6509	469	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691385.1	s__UBA4465 sp002691385	83.0123	618	1038	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:46,860] [INFO] GTDB search result was written to OceanDNA-b4197/result_gtdb.tsv
[2023-03-18 08:33:46,860] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:46,860] [INFO] DFAST_QC result json was written to OceanDNA-b4197/dqc_result.json
[2023-03-18 08:33:46,860] [INFO] DFAST_QC completed!
[2023-03-18 08:33:46,860] [INFO] Total running time: 0h1m51s