[2023-03-14 14:50:59,114] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:50:59,114] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:50:59,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference
[2023-03-14 14:51:00,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:51:00,213] [INFO] Task started: Prodigal
[2023-03-14 14:51:00,213] [INFO] Running command: cat /var/lib/cwl/stg1159992e-e452-4b47-8553-3bfb3295ae47/OceanDNA-b5050.fa | prodigal -d OceanDNA-b5050/cds.fna -a OceanDNA-b5050/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:51:04,690] [INFO] Task succeeded: Prodigal
[2023-03-14 14:51:04,691] [INFO] Task started: HMMsearch
[2023-03-14 14:51:04,691] [INFO] Running command: hmmsearch --tblout OceanDNA-b5050/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference/reference_markers.hmm OceanDNA-b5050/protein.faa > /dev/null
[2023-03-14 14:51:04,878] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:51:04,879] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1159992e-e452-4b47-8553-3bfb3295ae47/OceanDNA-b5050.fa]
[2023-03-14 14:51:04,891] [INFO] Query marker FASTA was written to OceanDNA-b5050/markers.fasta
[2023-03-14 14:51:04,892] [INFO] Task started: Blastn
[2023-03-14 14:51:04,892] [INFO] Running command: blastn -query OceanDNA-b5050/markers.fasta -db /var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference/reference_markers.fasta -out OceanDNA-b5050/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:51:05,450] [INFO] Task succeeded: Blastn
[2023-03-14 14:51:05,452] [INFO] Selected 26 target genomes.
[2023-03-14 14:51:05,452] [INFO] Target genome list was writen to OceanDNA-b5050/target_genomes.txt
[2023-03-14 14:51:05,464] [INFO] Task started: fastANI
[2023-03-14 14:51:05,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg1159992e-e452-4b47-8553-3bfb3295ae47/OceanDNA-b5050.fa --refList OceanDNA-b5050/target_genomes.txt --output OceanDNA-b5050/fastani_result.tsv --threads 1
[2023-03-14 14:51:27,716] [INFO] Task succeeded: fastANI
[2023-03-14 14:51:27,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:51:27,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:51:27,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:51:27,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:51:27,717] [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 14:51:27,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5050/tc_result.tsv
[2023-03-14 14:51:27,718] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:51:27,718] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:51:27,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference/checkm_data
[2023-03-14 14:51:27,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:51:27,738] [INFO] Task started: CheckM
[2023-03-14 14:51:27,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5050/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5050/checkm_input OceanDNA-b5050/checkm_result
[2023-03-14 14:51:48,684] [INFO] Task succeeded: CheckM
[2023-03-14 14:51:48,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.12%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:51:48,686] [INFO] ===== Completeness check finished =====
[2023-03-14 14:51:48,686] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:51:48,687] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5050/markers.fasta)
[2023-03-14 14:51:48,688] [INFO] Task started: Blastn
[2023-03-14 14:51:48,688] [INFO] Running command: blastn -query OceanDNA-b5050/markers.fasta -db /var/lib/cwl/stg0b89f500-6106-4eab-b115-6f8605e2c569/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5050/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:51:49,457] [INFO] Task succeeded: Blastn
[2023-03-14 14:51:49,458] [INFO] Selected 27 target genomes.
[2023-03-14 14:51:49,458] [INFO] Target genome list was writen to OceanDNA-b5050/target_genomes_gtdb.txt
[2023-03-14 14:51:49,539] [INFO] Task started: fastANI
[2023-03-14 14:51:49,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg1159992e-e452-4b47-8553-3bfb3295ae47/OceanDNA-b5050.fa --refList OceanDNA-b5050/target_genomes_gtdb.txt --output OceanDNA-b5050/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:51:56,736] [INFO] Task succeeded: fastANI
[2023-03-14 14:51:56,738] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:51:56,738] [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_002697505.1	s__GCA-2697505 sp002697505	95.2604	129	134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002728175.1	s__GCA-2697505 sp002728175	93.3316	133	134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:51:56,739] [INFO] GTDB search result was written to OceanDNA-b5050/result_gtdb.tsv
[2023-03-14 14:51:56,739] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:51:56,739] [INFO] DFAST_QC result json was written to OceanDNA-b5050/dqc_result.json
[2023-03-14 14:51:56,739] [INFO] DFAST_QC completed!
[2023-03-14 14:51:56,739] [INFO] Total running time: 0h0m58s