[2023-03-14 11:26:25,354] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:26:25,355] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:26:25,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference
[2023-03-14 11:26:27,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:26:27,360] [INFO] Task started: Prodigal
[2023-03-14 11:26:27,360] [INFO] Running command: cat /var/lib/cwl/stg9098ccbb-080e-45e3-8763-9609b02017ea/OceanDNA-b17348.fa | prodigal -d OceanDNA-b17348/cds.fna -a OceanDNA-b17348/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:26:45,671] [INFO] Task succeeded: Prodigal
[2023-03-14 11:26:45,671] [INFO] Task started: HMMsearch
[2023-03-14 11:26:45,671] [INFO] Running command: hmmsearch --tblout OceanDNA-b17348/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference/reference_markers.hmm OceanDNA-b17348/protein.faa > /dev/null
[2023-03-14 11:26:45,863] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:26:45,863] [INFO] Found 6/6 markers.
[2023-03-14 11:26:45,908] [INFO] Query marker FASTA was written to OceanDNA-b17348/markers.fasta
[2023-03-14 11:26:45,909] [INFO] Task started: Blastn
[2023-03-14 11:26:45,909] [INFO] Running command: blastn -query OceanDNA-b17348/markers.fasta -db /var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference/reference_markers.fasta -out OceanDNA-b17348/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:26:46,536] [INFO] Task succeeded: Blastn
[2023-03-14 11:26:46,545] [INFO] Selected 26 target genomes.
[2023-03-14 11:26:46,546] [INFO] Target genome list was writen to OceanDNA-b17348/target_genomes.txt
[2023-03-14 11:26:46,558] [INFO] Task started: fastANI
[2023-03-14 11:26:46,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg9098ccbb-080e-45e3-8763-9609b02017ea/OceanDNA-b17348.fa --refList OceanDNA-b17348/target_genomes.txt --output OceanDNA-b17348/fastani_result.tsv --threads 1
[2023-03-14 11:27:03,529] [INFO] Task succeeded: fastANI
[2023-03-14 11:27:03,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:27:03,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:27:03,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:27:03,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:27:03,530] [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
--------------------------------------------------------------------------------
[2023-03-14 11:27:03,533] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17348/tc_result.tsv
[2023-03-14 11:27:03,537] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:27:03,537] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:27:03,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference/checkm_data
[2023-03-14 11:27:03,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:27:03,551] [INFO] Task started: CheckM
[2023-03-14 11:27:03,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17348/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17348/checkm_input OceanDNA-b17348/checkm_result
[2023-03-14 11:27:51,076] [INFO] Task succeeded: CheckM
[2023-03-14 11:27:51,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:27:51,127] [INFO] ===== Completeness check finished =====
[2023-03-14 11:27:51,127] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:27:51,127] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17348/markers.fasta)
[2023-03-14 11:27:51,128] [INFO] Task started: Blastn
[2023-03-14 11:27:51,128] [INFO] Running command: blastn -query OceanDNA-b17348/markers.fasta -db /var/lib/cwl/stg77ea18d0-e692-4616-bb44-ee7661b59205/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17348/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:27:52,189] [INFO] Task succeeded: Blastn
[2023-03-14 11:27:52,201] [INFO] Selected 22 target genomes.
[2023-03-14 11:27:52,201] [INFO] Target genome list was writen to OceanDNA-b17348/target_genomes_gtdb.txt
[2023-03-14 11:27:52,242] [INFO] Task started: fastANI
[2023-03-14 11:27:52,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg9098ccbb-080e-45e3-8763-9609b02017ea/OceanDNA-b17348.fa --refList OceanDNA-b17348/target_genomes_gtdb.txt --output OceanDNA-b17348/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:28:04,252] [INFO] Task succeeded: fastANI
[2023-03-14 11:28:04,259] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:28:04,259] [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_002390225.1	s__UBA2589 sp002390225	99.773	918	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013002885.1	s__UBA2589 sp013002885	76.6541	165	982	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	76.5516	108	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937285.1	s__UBA1138 sp009937285	76.5418	66	982	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	76.3255	103	982	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	76.201	117	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.0638	102	982	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_009841165.1	s__Bin94 sp009841165	75.9156	53	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	99.63	99.39	0.93	0.90	5	-
GCA_018678395.1	s__IDS-52 sp018678395	75.8741	73	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__IDS-52	95.0	98.28	98.28	0.76	0.76	2	-
GCA_007126575.1	s__SLBA01 sp007126575	75.854	50	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SLBA01	95.0	99.74	99.74	0.94	0.94	2	-
GCA_009840525.1	s__BD2-11 sp009840525	75.5889	66	982	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__BD2-11	95.0	96.09	95.11	0.90	0.85	6	-
--------------------------------------------------------------------------------
[2023-03-14 11:28:04,268] [INFO] GTDB search result was written to OceanDNA-b17348/result_gtdb.tsv
[2023-03-14 11:28:04,282] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:28:04,291] [INFO] DFAST_QC result json was written to OceanDNA-b17348/dqc_result.json
[2023-03-14 11:28:04,291] [INFO] DFAST_QC completed!
[2023-03-14 11:28:04,291] [INFO] Total running time: 0h1m39s