[2023-03-16 04:39:48,746] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:48,746] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:48,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference
[2023-03-16 04:39:49,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:49,819] [INFO] Task started: Prodigal
[2023-03-16 04:39:49,820] [INFO] Running command: cat /var/lib/cwl/stg452e3796-7135-4a70-92a6-899ca9fbe459/OceanDNA-b17216.fa | prodigal -d OceanDNA-b17216/cds.fna -a OceanDNA-b17216/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:40:11,841] [INFO] Task succeeded: Prodigal
[2023-03-16 04:40:11,841] [INFO] Task started: HMMsearch
[2023-03-16 04:40:11,841] [INFO] Running command: hmmsearch --tblout OceanDNA-b17216/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference/reference_markers.hmm OceanDNA-b17216/protein.faa > /dev/null
[2023-03-16 04:40:12,039] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:40:12,040] [INFO] Found 6/6 markers.
[2023-03-16 04:40:12,059] [INFO] Query marker FASTA was written to OceanDNA-b17216/markers.fasta
[2023-03-16 04:40:12,060] [INFO] Task started: Blastn
[2023-03-16 04:40:12,060] [INFO] Running command: blastn -query OceanDNA-b17216/markers.fasta -db /var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference/reference_markers.fasta -out OceanDNA-b17216/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:12,588] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:12,589] [INFO] Selected 30 target genomes.
[2023-03-16 04:40:12,589] [INFO] Target genome list was writen to OceanDNA-b17216/target_genomes.txt
[2023-03-16 04:40:12,604] [INFO] Task started: fastANI
[2023-03-16 04:40:12,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg452e3796-7135-4a70-92a6-899ca9fbe459/OceanDNA-b17216.fa --refList OceanDNA-b17216/target_genomes.txt --output OceanDNA-b17216/fastani_result.tsv --threads 1
[2023-03-16 04:40:31,749] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:31,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:40:31,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:40:31,750] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:40:31,750] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:40:31,750] [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
--------------------------------------------------------------------------------
[2023-03-16 04:40:31,750] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17216/tc_result.tsv
[2023-03-16 04:40:31,751] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:40:31,751] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:40:31,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference/checkm_data
[2023-03-16 04:40:31,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:40:31,832] [INFO] Task started: CheckM
[2023-03-16 04:40:31,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17216/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17216/checkm_input OceanDNA-b17216/checkm_result
[2023-03-16 04:41:26,126] [INFO] Task succeeded: CheckM
[2023-03-16 04:41:26,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:41:26,129] [INFO] ===== Completeness check finished =====
[2023-03-16 04:41:26,129] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:41:26,129] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17216/markers.fasta)
[2023-03-16 04:41:26,130] [INFO] Task started: Blastn
[2023-03-16 04:41:26,130] [INFO] Running command: blastn -query OceanDNA-b17216/markers.fasta -db /var/lib/cwl/stgea82d837-12fa-48fd-8710-6871e7d6e9a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17216/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:41:26,875] [INFO] Task succeeded: Blastn
[2023-03-16 04:41:26,876] [INFO] Selected 27 target genomes.
[2023-03-16 04:41:26,876] [INFO] Target genome list was writen to OceanDNA-b17216/target_genomes_gtdb.txt
[2023-03-16 04:41:26,926] [INFO] Task started: fastANI
[2023-03-16 04:41:26,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg452e3796-7135-4a70-92a6-899ca9fbe459/OceanDNA-b17216.fa --refList OceanDNA-b17216/target_genomes_gtdb.txt --output OceanDNA-b17216/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:41:41,192] [INFO] Task succeeded: fastANI
[2023-03-16 04:41:41,198] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:41:41,198] [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_009937285.1	s__UBA1138 sp009937285	78.0571	153	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.12	98.44	0.93	0.79	16	-
GCA_009692205.1	s__UBA2982 sp009692205	76.76	96	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015664885.1	s__UBA1138 sp003447875	76.7359	144	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_013002885.1	s__UBA2589 sp013002885	76.6248	85	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_016873995.1	s__UBA2982 sp016873995	76.5277	96	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.2306	103	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015492755.1	s__S146-37 sp015492755	76.1833	81	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__S146-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840525.1	s__BD2-11 sp009840525	75.7668	50	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	96.09	95.11	0.90	0.85	6	-
GCA_018678395.1	s__IDS-52 sp018678395	75.4247	50	1171	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__IDS-52	95.0	98.28	98.28	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:41:41,198] [INFO] GTDB search result was written to OceanDNA-b17216/result_gtdb.tsv
[2023-03-16 04:41:41,198] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:41:41,199] [INFO] DFAST_QC result json was written to OceanDNA-b17216/dqc_result.json
[2023-03-16 04:41:41,199] [INFO] DFAST_QC completed!
[2023-03-16 04:41:41,199] [INFO] Total running time: 0h1m52s