[2023-03-18 20:55:47,243] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,243] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference
[2023-03-18 20:55:48,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,399] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,400] [INFO] Running command: cat /var/lib/cwl/stg2f64561b-6b8e-4cee-bba1-3404bd8d9534/OceanDNA-b22226.fa | prodigal -d OceanDNA-b22226/cds.fna -a OceanDNA-b22226/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:56:05,213] [INFO] Task succeeded: Prodigal
[2023-03-18 20:56:05,213] [INFO] Task started: HMMsearch
[2023-03-18 20:56:05,213] [INFO] Running command: hmmsearch --tblout OceanDNA-b22226/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference/reference_markers.hmm OceanDNA-b22226/protein.faa > /dev/null
[2023-03-18 20:56:05,397] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:56:05,398] [INFO] Found 6/6 markers.
[2023-03-18 20:56:05,413] [INFO] Query marker FASTA was written to OceanDNA-b22226/markers.fasta
[2023-03-18 20:56:05,414] [INFO] Task started: Blastn
[2023-03-18 20:56:05,414] [INFO] Running command: blastn -query OceanDNA-b22226/markers.fasta -db /var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference/reference_markers.fasta -out OceanDNA-b22226/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:05,923] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:05,924] [INFO] Selected 25 target genomes.
[2023-03-18 20:56:05,924] [INFO] Target genome list was writen to OceanDNA-b22226/target_genomes.txt
[2023-03-18 20:56:05,937] [INFO] Task started: fastANI
[2023-03-18 20:56:05,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f64561b-6b8e-4cee-bba1-3404bd8d9534/OceanDNA-b22226.fa --refList OceanDNA-b22226/target_genomes.txt --output OceanDNA-b22226/fastani_result.tsv --threads 1
[2023-03-18 20:56:21,972] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:21,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:21,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:21,973] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:21,973] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:56:21,973] [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
--------------------------------------------------------------------------------
[2023-03-18 20:56:21,973] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22226/tc_result.tsv
[2023-03-18 20:56:21,973] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:21,974] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:21,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference/checkm_data
[2023-03-18 20:56:21,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:21,980] [INFO] Task started: CheckM
[2023-03-18 20:56:21,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22226/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22226/checkm_input OceanDNA-b22226/checkm_result
[2023-03-18 20:57:07,914] [INFO] Task succeeded: CheckM
[2023-03-18 20:57:07,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:57:07,917] [INFO] ===== Completeness check finished =====
[2023-03-18 20:57:07,917] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:57:07,917] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22226/markers.fasta)
[2023-03-18 20:57:07,917] [INFO] Task started: Blastn
[2023-03-18 20:57:07,917] [INFO] Running command: blastn -query OceanDNA-b22226/markers.fasta -db /var/lib/cwl/stg05702696-298f-4f25-8abe-9b17034ddd3a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22226/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:57:08,598] [INFO] Task succeeded: Blastn
[2023-03-18 20:57:08,599] [INFO] Selected 17 target genomes.
[2023-03-18 20:57:08,599] [INFO] Target genome list was writen to OceanDNA-b22226/target_genomes_gtdb.txt
[2023-03-18 20:57:08,809] [INFO] Task started: fastANI
[2023-03-18 20:57:08,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f64561b-6b8e-4cee-bba1-3404bd8d9534/OceanDNA-b22226.fa --refList OceanDNA-b22226/target_genomes_gtdb.txt --output OceanDNA-b22226/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:57:16,821] [INFO] Task succeeded: fastANI
[2023-03-18 20:57:16,826] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:57:16,827] [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_002716385.1	s__UBA1668 sp002716385	99.937	802	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002364555.1	s__UBA1668 sp002364555	80.94	551	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702575.1	s__UBA1668 sp002702575	77.9101	274	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	99.83	99.83	0.97	0.97	3	-
GCA_002717655.1	s__UBA1668 sp002717655	77.3534	167	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364485.1	s__UBA854 sp002364485	76.7697	89	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.87	99.87	0.97	0.97	2	-
GCA_002295885.1	s__UBA854 sp002295885	76.6583	87	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.78	99.78	0.94	0.94	2	-
GCA_002722935.1	s__SP202 sp002722935	76.4409	51	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002591705.1	s__UBA854 sp002591705	76.2252	61	875	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:57:16,827] [INFO] GTDB search result was written to OceanDNA-b22226/result_gtdb.tsv
[2023-03-18 20:57:16,827] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:57:16,828] [INFO] DFAST_QC result json was written to OceanDNA-b22226/dqc_result.json
[2023-03-18 20:57:16,828] [INFO] DFAST_QC completed!
[2023-03-18 20:57:16,828] [INFO] Total running time: 0h1m30s