[2023-03-18 10:46:22,078] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:46:22,083] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:46:22,083] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference
[2023-03-18 10:46:23,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:46:23,266] [INFO] Task started: Prodigal
[2023-03-18 10:46:23,267] [INFO] Running command: cat /var/lib/cwl/stg158c8968-bf5b-4a86-a67e-cb30d25b0e61/OceanDNA-b7115.fa | prodigal -d OceanDNA-b7115/cds.fna -a OceanDNA-b7115/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:46:31,235] [INFO] Task succeeded: Prodigal
[2023-03-18 10:46:31,236] [INFO] Task started: HMMsearch
[2023-03-18 10:46:31,236] [INFO] Running command: hmmsearch --tblout OceanDNA-b7115/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference/reference_markers.hmm OceanDNA-b7115/protein.faa > /dev/null
[2023-03-18 10:46:31,401] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:46:31,402] [INFO] Found 6/6 markers.
[2023-03-18 10:46:31,438] [INFO] Query marker FASTA was written to OceanDNA-b7115/markers.fasta
[2023-03-18 10:46:31,440] [INFO] Task started: Blastn
[2023-03-18 10:46:31,440] [INFO] Running command: blastn -query OceanDNA-b7115/markers.fasta -db /var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference/reference_markers.fasta -out OceanDNA-b7115/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:46:31,992] [INFO] Task succeeded: Blastn
[2023-03-18 10:46:32,007] [INFO] Selected 35 target genomes.
[2023-03-18 10:46:32,007] [INFO] Target genome list was writen to OceanDNA-b7115/target_genomes.txt
[2023-03-18 10:46:32,026] [INFO] Task started: fastANI
[2023-03-18 10:46:32,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg158c8968-bf5b-4a86-a67e-cb30d25b0e61/OceanDNA-b7115.fa --refList OceanDNA-b7115/target_genomes.txt --output OceanDNA-b7115/fastani_result.tsv --threads 1
[2023-03-18 10:46:50,915] [INFO] Task succeeded: fastANI
[2023-03-18 10:46:50,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:46:50,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:46:50,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:46:50,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:46:50,916] [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 10:46:50,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7115/tc_result.tsv
[2023-03-18 10:46:50,923] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:46:50,923] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:46:50,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference/checkm_data
[2023-03-18 10:46:50,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:46:50,969] [INFO] Task started: CheckM
[2023-03-18 10:46:50,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7115/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7115/checkm_input OceanDNA-b7115/checkm_result
[2023-03-18 10:47:15,998] [INFO] Task succeeded: CheckM
[2023-03-18 10:47:15,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:47:16,016] [INFO] ===== Completeness check finished =====
[2023-03-18 10:47:16,016] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:47:16,016] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7115/markers.fasta)
[2023-03-18 10:47:16,017] [INFO] Task started: Blastn
[2023-03-18 10:47:16,017] [INFO] Running command: blastn -query OceanDNA-b7115/markers.fasta -db /var/lib/cwl/stg6dbde169-33ef-4320-9073-bc72db25e5e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7115/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:47:16,793] [INFO] Task succeeded: Blastn
[2023-03-18 10:47:16,799] [INFO] Selected 30 target genomes.
[2023-03-18 10:47:16,799] [INFO] Target genome list was writen to OceanDNA-b7115/target_genomes_gtdb.txt
[2023-03-18 10:47:16,825] [INFO] Task started: fastANI
[2023-03-18 10:47:16,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg158c8968-bf5b-4a86-a67e-cb30d25b0e61/OceanDNA-b7115.fa --refList OceanDNA-b7115/target_genomes_gtdb.txt --output OceanDNA-b7115/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:47:26,042] [INFO] Task succeeded: fastANI
[2023-03-18 10:47:26,046] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:47:26,047] [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_002719315.1	s__GCA-2719315 sp002719315	91.5412	421	437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560065.1	s__GCA-2719315 sp902560065	91.454	248	437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728855.1	s__GCA-002728855 sp002728855	76.4617	81	437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002728855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	76.1091	53	437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	75.988	60	437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905381055.1	s__TMED220 sp905381055	75.3907	83	437	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:47:26,049] [INFO] GTDB search result was written to OceanDNA-b7115/result_gtdb.tsv
[2023-03-18 10:47:26,054] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:47:26,059] [INFO] DFAST_QC result json was written to OceanDNA-b7115/dqc_result.json
[2023-03-18 10:47:26,059] [INFO] DFAST_QC completed!
[2023-03-18 10:47:26,059] [INFO] Total running time: 0h1m4s