[2023-03-15 10:21:46,235] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference
[2023-03-15 10:21:47,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,936] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,936] [INFO] Running command: cat /var/lib/cwl/stgc357d7b4-353a-4254-a44a-2cf8db8862e6/OceanDNA-b12909.fa | prodigal -d OceanDNA-b12909/cds.fna -a OceanDNA-b12909/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:22:10,867] [INFO] Task succeeded: Prodigal
[2023-03-15 10:22:10,867] [INFO] Task started: HMMsearch
[2023-03-15 10:22:10,867] [INFO] Running command: hmmsearch --tblout OceanDNA-b12909/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference/reference_markers.hmm OceanDNA-b12909/protein.faa > /dev/null
[2023-03-15 10:22:11,068] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:11,069] [INFO] Found 6/6 markers.
[2023-03-15 10:22:11,090] [INFO] Query marker FASTA was written to OceanDNA-b12909/markers.fasta
[2023-03-15 10:22:11,090] [INFO] Task started: Blastn
[2023-03-15 10:22:11,090] [INFO] Running command: blastn -query OceanDNA-b12909/markers.fasta -db /var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference/reference_markers.fasta -out OceanDNA-b12909/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:11,613] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:11,613] [INFO] Selected 23 target genomes.
[2023-03-15 10:22:11,614] [INFO] Target genome list was writen to OceanDNA-b12909/target_genomes.txt
[2023-03-15 10:22:11,628] [INFO] Task started: fastANI
[2023-03-15 10:22:11,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgc357d7b4-353a-4254-a44a-2cf8db8862e6/OceanDNA-b12909.fa --refList OceanDNA-b12909/target_genomes.txt --output OceanDNA-b12909/fastani_result.tsv --threads 1
[2023-03-15 10:22:23,401] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:23,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:23,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:23,404] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:23,404] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:23,404] [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
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	76.9096	103	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:23,404] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12909/tc_result.tsv
[2023-03-15 10:22:23,404] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:23,404] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:23,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference/checkm_data
[2023-03-15 10:22:23,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:23,414] [INFO] Task started: CheckM
[2023-03-15 10:22:23,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12909/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12909/checkm_input OceanDNA-b12909/checkm_result
[2023-03-15 10:23:20,341] [INFO] Task succeeded: CheckM
[2023-03-15 10:23:20,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:23:20,344] [INFO] ===== Completeness check finished =====
[2023-03-15 10:23:20,345] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:23:20,345] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12909/markers.fasta)
[2023-03-15 10:23:20,345] [INFO] Task started: Blastn
[2023-03-15 10:23:20,345] [INFO] Running command: blastn -query OceanDNA-b12909/markers.fasta -db /var/lib/cwl/stg6148066a-2ae1-471b-ad1c-c2a1d6e6035e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12909/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:23:21,102] [INFO] Task succeeded: Blastn
[2023-03-15 10:23:21,103] [INFO] Selected 22 target genomes.
[2023-03-15 10:23:21,103] [INFO] Target genome list was writen to OceanDNA-b12909/target_genomes_gtdb.txt
[2023-03-15 10:23:21,816] [INFO] Task started: fastANI
[2023-03-15 10:23:21,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgc357d7b4-353a-4254-a44a-2cf8db8862e6/OceanDNA-b12909.fa --refList OceanDNA-b12909/target_genomes_gtdb.txt --output OceanDNA-b12909/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:23:32,674] [INFO] Task succeeded: fastANI
[2023-03-15 10:23:32,681] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:23:32,681] [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
GCF_000375465.1	s__Balneola vulgaris	76.9096	103	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643645.1	s__Balneola sp017643645	76.8522	106	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.99	99.98	1.00	0.99	5	-
GCA_006969905.1	s__Balneola sp006969905	76.8226	95	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364085.1	s__Balneola sp002364085	76.7373	117	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
GCA_017640785.1	s__Balneola sp017640785	76.7235	120	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650905.1	s__Balneola sp001650905	76.4805	120	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	96.92	96.92	0.89	0.89	2	-
GCA_017643365.1	s__HXMU1420-13 sp017643365	76.4554	84	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640605.1	s__HXMU1420-13 sp017640605	76.1937	74	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694685.1	s__Gracilimonas sp002694685	76.1314	81	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_017795005.1	s__RHLJ01 sp017795005	76.1246	80	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480645.1	s__UBA7797 sp002480645	76.0461	60	1150	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA7797	95.0	99.98	99.91	0.99	0.98	7	-
--------------------------------------------------------------------------------
[2023-03-15 10:23:32,682] [INFO] GTDB search result was written to OceanDNA-b12909/result_gtdb.tsv
[2023-03-15 10:23:32,682] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:23:32,683] [INFO] DFAST_QC result json was written to OceanDNA-b12909/dqc_result.json
[2023-03-15 10:23:32,683] [INFO] DFAST_QC completed!
[2023-03-15 10:23:32,683] [INFO] Total running time: 0h1m46s