[2023-03-18 03:09:33,834] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,834] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference
[2023-03-18 03:09:34,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,926] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,926] [INFO] Running command: cat /var/lib/cwl/stg2ffd7c2b-c8b6-41cb-9b0f-642b732b386f/OceanDNA-b11232.fa | prodigal -d OceanDNA-b11232/cds.fna -a OceanDNA-b11232/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:42,296] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:42,296] [INFO] Task started: HMMsearch
[2023-03-18 03:09:42,297] [INFO] Running command: hmmsearch --tblout OceanDNA-b11232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference/reference_markers.hmm OceanDNA-b11232/protein.faa > /dev/null
[2023-03-18 03:09:42,461] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:42,461] [INFO] Found 6/6 markers.
[2023-03-18 03:09:42,471] [INFO] Query marker FASTA was written to OceanDNA-b11232/markers.fasta
[2023-03-18 03:09:42,471] [INFO] Task started: Blastn
[2023-03-18 03:09:42,472] [INFO] Running command: blastn -query OceanDNA-b11232/markers.fasta -db /var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference/reference_markers.fasta -out OceanDNA-b11232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:43,010] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:43,011] [INFO] Selected 27 target genomes.
[2023-03-18 03:09:43,011] [INFO] Target genome list was writen to OceanDNA-b11232/target_genomes.txt
[2023-03-18 03:09:43,025] [INFO] Task started: fastANI
[2023-03-18 03:09:43,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ffd7c2b-c8b6-41cb-9b0f-642b732b386f/OceanDNA-b11232.fa --refList OceanDNA-b11232/target_genomes.txt --output OceanDNA-b11232/fastani_result.tsv --threads 1
[2023-03-18 03:09:56,771] [INFO] Task succeeded: fastANI
[2023-03-18 03:09:56,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:09:56,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:09:56,771] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:09:56,771] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:09:56,772] [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 03:09:56,772] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11232/tc_result.tsv
[2023-03-18 03:09:56,772] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:09:56,772] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:09:56,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference/checkm_data
[2023-03-18 03:09:56,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:09:56,777] [INFO] Task started: CheckM
[2023-03-18 03:09:56,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11232/checkm_input OceanDNA-b11232/checkm_result
[2023-03-18 03:10:21,133] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:21,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.87%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:21,135] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:21,135] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:21,135] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11232/markers.fasta)
[2023-03-18 03:10:21,136] [INFO] Task started: Blastn
[2023-03-18 03:10:21,136] [INFO] Running command: blastn -query OceanDNA-b11232/markers.fasta -db /var/lib/cwl/stg4ed09d4f-d508-4082-a2f7-e67595e6672a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:21,966] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:21,966] [INFO] Selected 12 target genomes.
[2023-03-18 03:10:21,966] [INFO] Target genome list was writen to OceanDNA-b11232/target_genomes_gtdb.txt
[2023-03-18 03:10:22,025] [INFO] Task started: fastANI
[2023-03-18 03:10:22,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ffd7c2b-c8b6-41cb-9b0f-642b732b386f/OceanDNA-b11232.fa --refList OceanDNA-b11232/target_genomes_gtdb.txt --output OceanDNA-b11232/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:25,508] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:25,513] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:10:25,513] [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_902619315.1	s__UBA8316 sp902619315	92.5504	196	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687665.1	s__UBA8316 sp002687665	92.4158	188	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623955.1	s__UBA8316 sp018623955	84.502	133	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364535.1	s__UBA8316 sp002364535	80.904	202	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002336305.1	s__UBA8316 sp002336305	80.7445	155	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	79.2343	162	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002390455.1	s__UBA8316 sp002390455	78.8357	171	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_018647605.1	s__UBA8316 sp018647605	77.6439	91	285	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:25,514] [INFO] GTDB search result was written to OceanDNA-b11232/result_gtdb.tsv
[2023-03-18 03:10:25,514] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:25,514] [INFO] DFAST_QC result json was written to OceanDNA-b11232/dqc_result.json
[2023-03-18 03:10:25,515] [INFO] DFAST_QC completed!
[2023-03-18 03:10:25,515] [INFO] Total running time: 0h0m52s