[2023-03-16 09:47:30,747] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:47:30,747] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:47:30,747] [INFO] DQC Reference Directory: /var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference
[2023-03-16 09:47:31,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:47:31,850] [INFO] Task started: Prodigal
[2023-03-16 09:47:31,850] [INFO] Running command: cat /var/lib/cwl/stg64d6838d-7fc6-4c73-822a-5c14b8bf31b8/OceanDNA-b13049.fa | prodigal -d OceanDNA-b13049/cds.fna -a OceanDNA-b13049/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:47:52,381] [INFO] Task succeeded: Prodigal
[2023-03-16 09:47:52,381] [INFO] Task started: HMMsearch
[2023-03-16 09:47:52,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b13049/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference/reference_markers.hmm OceanDNA-b13049/protein.faa > /dev/null
[2023-03-16 09:47:52,569] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:47:52,570] [INFO] Found 6/6 markers.
[2023-03-16 09:47:52,590] [INFO] Query marker FASTA was written to OceanDNA-b13049/markers.fasta
[2023-03-16 09:47:52,591] [INFO] Task started: Blastn
[2023-03-16 09:47:52,591] [INFO] Running command: blastn -query OceanDNA-b13049/markers.fasta -db /var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference/reference_markers.fasta -out OceanDNA-b13049/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:47:53,105] [INFO] Task succeeded: Blastn
[2023-03-16 09:47:53,108] [INFO] Selected 22 target genomes.
[2023-03-16 09:47:53,108] [INFO] Target genome list was writen to OceanDNA-b13049/target_genomes.txt
[2023-03-16 09:47:53,226] [INFO] Task started: fastANI
[2023-03-16 09:47:53,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg64d6838d-7fc6-4c73-822a-5c14b8bf31b8/OceanDNA-b13049.fa --refList OceanDNA-b13049/target_genomes.txt --output OceanDNA-b13049/fastani_result.tsv --threads 1
[2023-03-16 09:48:05,303] [INFO] Task succeeded: fastANI
[2023-03-16 09:48:05,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:48:05,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:48:05,307] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:48:05,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:48:05,307] [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
Rhodohalobacter barkolensis	strain=15182	GCA_002834295.1	2053187	2053187	type	True	76.3326	68	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:48:05,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13049/tc_result.tsv
[2023-03-16 09:48:05,309] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:48:05,310] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:48:05,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference/checkm_data
[2023-03-16 09:48:05,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:48:05,376] [INFO] Task started: CheckM
[2023-03-16 09:48:05,376] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13049/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13049/checkm_input OceanDNA-b13049/checkm_result
[2023-03-16 09:49:00,043] [INFO] Task succeeded: CheckM
[2023-03-16 09:49:00,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:49:00,046] [INFO] ===== Completeness check finished =====
[2023-03-16 09:49:00,046] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:49:00,047] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13049/markers.fasta)
[2023-03-16 09:49:00,048] [INFO] Task started: Blastn
[2023-03-16 09:49:00,048] [INFO] Running command: blastn -query OceanDNA-b13049/markers.fasta -db /var/lib/cwl/stga5f439c8-d0a2-4f61-996d-73bceba06eae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13049/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:49:00,781] [INFO] Task succeeded: Blastn
[2023-03-16 09:49:00,782] [INFO] Selected 19 target genomes.
[2023-03-16 09:49:00,782] [INFO] Target genome list was writen to OceanDNA-b13049/target_genomes_gtdb.txt
[2023-03-16 09:49:00,799] [INFO] Task started: fastANI
[2023-03-16 09:49:00,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg64d6838d-7fc6-4c73-822a-5c14b8bf31b8/OceanDNA-b13049.fa --refList OceanDNA-b13049/target_genomes_gtdb.txt --output OceanDNA-b13049/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:49:11,396] [INFO] Task succeeded: fastANI
[2023-03-16 09:49:11,404] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:49:11,404] [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_002359315.1	s__UBA2664 sp002359315	99.9569	772	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007123715.1	s__UBA2664 sp007123715	76.6858	60	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	98.93	98.93	0.91	0.91	2	-
GCA_007123785.1	s__UBA2664 sp007123785	76.6222	55	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	98.99	98.99	0.79	0.79	2	-
GCA_007131725.1	s__UBA2664 sp007131725	76.3606	66	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834295.1	s__Rhodohalobacter barkolensis	76.3326	68	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Rhodohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134085.1	s__UBA2664 sp007134085	76.2819	62	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.68	99.40	0.90	0.85	6	-
GCA_001564065.1	s__Rhodohalobacter sp001564065	76.223	63	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Rhodohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135335.1	s__UBA2664 sp007135335	76.2157	72	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.26	99.26	0.85	0.85	2	-
GCA_007693395.1	s__UBA2664 sp007693395	76.1761	74	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127745.1	s__UBA2664 sp007127745	76.1722	71	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.25	98.53	0.84	0.77	4	-
GCA_007123985.1	s__UBA2664 sp007123985	76.1472	70	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	99.06	99.06	0.82	0.82	2	-
GCA_007694095.1	s__UBA2664 sp007694095	75.9087	70	956	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__UBA2664	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:49:11,437] [INFO] GTDB search result was written to OceanDNA-b13049/result_gtdb.tsv
[2023-03-16 09:49:11,664] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:49:11,665] [INFO] DFAST_QC result json was written to OceanDNA-b13049/dqc_result.json
[2023-03-16 09:49:11,665] [INFO] DFAST_QC completed!
[2023-03-16 09:49:11,665] [INFO] Total running time: 0h1m41s