[2023-03-19 01:33:27,156] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,156] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,156] [INFO] DQC Reference Directory: /var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference
[2023-03-19 01:33:28,251] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,252] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,252] [INFO] Running command: cat /var/lib/cwl/stgfd94f9c2-effd-4fe4-bc77-34e7e447b1be/OceanDNA-b11567.fa | prodigal -d OceanDNA-b11567/cds.fna -a OceanDNA-b11567/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:37,149] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:37,149] [INFO] Task started: HMMsearch
[2023-03-19 01:33:37,149] [INFO] Running command: hmmsearch --tblout OceanDNA-b11567/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference/reference_markers.hmm OceanDNA-b11567/protein.faa > /dev/null
[2023-03-19 01:33:37,358] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:37,358] [INFO] Found 6/6 markers.
[2023-03-19 01:33:37,369] [INFO] Query marker FASTA was written to OceanDNA-b11567/markers.fasta
[2023-03-19 01:33:37,369] [INFO] Task started: Blastn
[2023-03-19 01:33:37,369] [INFO] Running command: blastn -query OceanDNA-b11567/markers.fasta -db /var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference/reference_markers.fasta -out OceanDNA-b11567/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:37,942] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:37,943] [INFO] Selected 27 target genomes.
[2023-03-19 01:33:37,943] [INFO] Target genome list was writen to OceanDNA-b11567/target_genomes.txt
[2023-03-19 01:33:37,962] [INFO] Task started: fastANI
[2023-03-19 01:33:37,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd94f9c2-effd-4fe4-bc77-34e7e447b1be/OceanDNA-b11567.fa --refList OceanDNA-b11567/target_genomes.txt --output OceanDNA-b11567/fastani_result.tsv --threads 1
[2023-03-19 01:33:50,565] [INFO] Task succeeded: fastANI
[2023-03-19 01:33:50,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:33:50,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:33:50,566] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:33:50,566] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:33:50,566] [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
--------------------------------------------------------------------------------
[2023-03-19 01:33:50,566] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11567/tc_result.tsv
[2023-03-19 01:33:50,566] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:33:50,566] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:33:50,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference/checkm_data
[2023-03-19 01:33:50,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:33:50,573] [INFO] Task started: CheckM
[2023-03-19 01:33:50,573] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11567/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11567/checkm_input OceanDNA-b11567/checkm_result
[2023-03-19 01:34:17,473] [INFO] Task succeeded: CheckM
[2023-03-19 01:34:17,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:34:17,475] [INFO] ===== Completeness check finished =====
[2023-03-19 01:34:17,475] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:34:17,475] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11567/markers.fasta)
[2023-03-19 01:34:17,476] [INFO] Task started: Blastn
[2023-03-19 01:34:17,476] [INFO] Running command: blastn -query OceanDNA-b11567/markers.fasta -db /var/lib/cwl/stgddb124f7-92d9-46e4-8c77-2573098f06b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11567/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:34:18,392] [INFO] Task succeeded: Blastn
[2023-03-19 01:34:18,393] [INFO] Selected 20 target genomes.
[2023-03-19 01:34:18,393] [INFO] Target genome list was writen to OceanDNA-b11567/target_genomes_gtdb.txt
[2023-03-19 01:34:18,412] [INFO] Task started: fastANI
[2023-03-19 01:34:18,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd94f9c2-effd-4fe4-bc77-34e7e447b1be/OceanDNA-b11567.fa --refList OceanDNA-b11567/target_genomes_gtdb.txt --output OceanDNA-b11567/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:34:24,513] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:24,519] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:34:24,519] [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_002701365.1	s__GCA-002701365 sp002701365	99.8996	465	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002713285.1	s__SP256 sp002713285	77.5189	172	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	77.5126	162	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722215.1	s__SP256 sp002722215	77.1811	149	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	77.0958	124	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696965.1	s__GCA-2696965 sp002696965	76.9501	76	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.8921	124	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698365.1	s__GCA-002707245 sp002698365	76.761	97	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718895.1	s__GCA-2718895 sp002718895	76.4299	89	485	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718895	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:34:24,519] [INFO] GTDB search result was written to OceanDNA-b11567/result_gtdb.tsv
[2023-03-19 01:34:24,519] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:34:24,520] [INFO] DFAST_QC result json was written to OceanDNA-b11567/dqc_result.json
[2023-03-19 01:34:24,520] [INFO] DFAST_QC completed!
[2023-03-19 01:34:24,520] [INFO] Total running time: 0h0m57s