[2023-03-18 03:59:27,744] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:27,745] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:27,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference
[2023-03-18 03:59:29,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:29,370] [INFO] Task started: Prodigal
[2023-03-18 03:59:29,370] [INFO] Running command: cat /var/lib/cwl/stgc67e1ee1-813a-4b6c-8203-ec2f6065a2c5/OceanDNA-b22222.fa | prodigal -d OceanDNA-b22222/cds.fna -a OceanDNA-b22222/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:46,364] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:46,365] [INFO] Task started: HMMsearch
[2023-03-18 03:59:46,365] [INFO] Running command: hmmsearch --tblout OceanDNA-b22222/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference/reference_markers.hmm OceanDNA-b22222/protein.faa > /dev/null
[2023-03-18 03:59:46,542] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:46,542] [INFO] Found 6/6 markers.
[2023-03-18 03:59:46,560] [INFO] Query marker FASTA was written to OceanDNA-b22222/markers.fasta
[2023-03-18 03:59:46,560] [INFO] Task started: Blastn
[2023-03-18 03:59:46,560] [INFO] Running command: blastn -query OceanDNA-b22222/markers.fasta -db /var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference/reference_markers.fasta -out OceanDNA-b22222/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:47,083] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:47,083] [INFO] Selected 21 target genomes.
[2023-03-18 03:59:47,084] [INFO] Target genome list was writen to OceanDNA-b22222/target_genomes.txt
[2023-03-18 03:59:47,096] [INFO] Task started: fastANI
[2023-03-18 03:59:47,096] [INFO] Running command: fastANI --query /var/lib/cwl/stgc67e1ee1-813a-4b6c-8203-ec2f6065a2c5/OceanDNA-b22222.fa --refList OceanDNA-b22222/target_genomes.txt --output OceanDNA-b22222/fastani_result.tsv --threads 1
[2023-03-18 04:00:08,526] [INFO] Task succeeded: fastANI
[2023-03-18 04:00:08,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:00:08,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:00:08,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:00:08,526] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:00:08,526] [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 04:00:08,527] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22222/tc_result.tsv
[2023-03-18 04:00:08,527] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:00:08,527] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:00:08,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference/checkm_data
[2023-03-18 04:00:08,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:00:08,533] [INFO] Task started: CheckM
[2023-03-18 04:00:08,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22222/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22222/checkm_input OceanDNA-b22222/checkm_result
[2023-03-18 04:01:16,698] [INFO] Task succeeded: CheckM
[2023-03-18 04:01:16,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:01:16,701] [INFO] ===== Completeness check finished =====
[2023-03-18 04:01:16,701] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:01:16,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22222/markers.fasta)
[2023-03-18 04:01:16,701] [INFO] Task started: Blastn
[2023-03-18 04:01:16,701] [INFO] Running command: blastn -query OceanDNA-b22222/markers.fasta -db /var/lib/cwl/stg10f95ab7-9c4e-4636-840e-b959118addca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22222/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:01:17,449] [INFO] Task succeeded: Blastn
[2023-03-18 04:01:17,450] [INFO] Selected 16 target genomes.
[2023-03-18 04:01:17,450] [INFO] Target genome list was writen to OceanDNA-b22222/target_genomes_gtdb.txt
[2023-03-18 04:01:17,555] [INFO] Task started: fastANI
[2023-03-18 04:01:17,555] [INFO] Running command: fastANI --query /var/lib/cwl/stgc67e1ee1-813a-4b6c-8203-ec2f6065a2c5/OceanDNA-b22222.fa --refList OceanDNA-b22222/target_genomes_gtdb.txt --output OceanDNA-b22222/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:01:26,857] [INFO] Task succeeded: fastANI
[2023-03-18 04:01:26,861] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:01:26,861] [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_002702575.1	s__UBA1668 sp002702575	99.8749	867	883	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	99.83	99.83	0.97	0.97	3	conclusive
GCA_002716385.1	s__UBA1668 sp002716385	78.0384	247	883	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717655.1	s__UBA1668 sp002717655	77.4995	196	883	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364555.1	s__UBA1668 sp002364555	77.4836	208	883	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	76.8809	69	883	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	76.4559	72	883	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.78	99.78	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-18 04:01:26,862] [INFO] GTDB search result was written to OceanDNA-b22222/result_gtdb.tsv
[2023-03-18 04:01:26,862] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:01:26,862] [INFO] DFAST_QC result json was written to OceanDNA-b22222/dqc_result.json
[2023-03-18 04:01:26,862] [INFO] DFAST_QC completed!
[2023-03-18 04:01:26,863] [INFO] Total running time: 0h1m59s