[2023-03-17 04:35:35,467] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:35:35,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:35:35,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference
[2023-03-17 04:35:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:35:36,687] [INFO] Task started: Prodigal
[2023-03-17 04:35:36,688] [INFO] Running command: cat /var/lib/cwl/stg02735fd8-ec62-4037-9576-71957b75036b/OceanDNA-b7111.fa | prodigal -d OceanDNA-b7111/cds.fna -a OceanDNA-b7111/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:35:42,421] [INFO] Task succeeded: Prodigal
[2023-03-17 04:35:42,421] [INFO] Task started: HMMsearch
[2023-03-17 04:35:42,421] [INFO] Running command: hmmsearch --tblout OceanDNA-b7111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference/reference_markers.hmm OceanDNA-b7111/protein.faa > /dev/null
[2023-03-17 04:35:42,584] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:35:42,585] [INFO] Found 6/6 markers.
[2023-03-17 04:35:42,594] [INFO] Query marker FASTA was written to OceanDNA-b7111/markers.fasta
[2023-03-17 04:35:42,594] [INFO] Task started: Blastn
[2023-03-17 04:35:42,594] [INFO] Running command: blastn -query OceanDNA-b7111/markers.fasta -db /var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference/reference_markers.fasta -out OceanDNA-b7111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:35:43,177] [INFO] Task succeeded: Blastn
[2023-03-17 04:35:43,178] [INFO] Selected 31 target genomes.
[2023-03-17 04:35:43,178] [INFO] Target genome list was writen to OceanDNA-b7111/target_genomes.txt
[2023-03-17 04:35:43,189] [INFO] Task started: fastANI
[2023-03-17 04:35:43,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg02735fd8-ec62-4037-9576-71957b75036b/OceanDNA-b7111.fa --refList OceanDNA-b7111/target_genomes.txt --output OceanDNA-b7111/fastani_result.tsv --threads 1
[2023-03-17 04:35:59,824] [INFO] Task succeeded: fastANI
[2023-03-17 04:35:59,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:35:59,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:35:59,825] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:35:59,825] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:35:59,825] [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
--------------------------------------------------------------------------------
[2023-03-17 04:35:59,825] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7111/tc_result.tsv
[2023-03-17 04:35:59,825] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:35:59,825] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:35:59,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference/checkm_data
[2023-03-17 04:35:59,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:35:59,830] [INFO] Task started: CheckM
[2023-03-17 04:35:59,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7111/checkm_input OceanDNA-b7111/checkm_result
[2023-03-17 04:36:19,803] [INFO] Task succeeded: CheckM
[2023-03-17 04:36:19,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:36:19,805] [INFO] ===== Completeness check finished =====
[2023-03-17 04:36:19,805] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:36:19,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7111/markers.fasta)
[2023-03-17 04:36:19,805] [INFO] Task started: Blastn
[2023-03-17 04:36:19,805] [INFO] Running command: blastn -query OceanDNA-b7111/markers.fasta -db /var/lib/cwl/stg4882d5d4-7f30-4868-8f6e-de5fe84f94a2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:36:20,812] [INFO] Task succeeded: Blastn
[2023-03-17 04:36:20,813] [INFO] Selected 27 target genomes.
[2023-03-17 04:36:20,813] [INFO] Target genome list was writen to OceanDNA-b7111/target_genomes_gtdb.txt
[2023-03-17 04:36:21,463] [INFO] Task started: fastANI
[2023-03-17 04:36:21,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg02735fd8-ec62-4037-9576-71957b75036b/OceanDNA-b7111.fa --refList OceanDNA-b7111/target_genomes_gtdb.txt --output OceanDNA-b7111/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:36:29,527] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:29,532] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:36:29,532] [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_902560065.1	s__GCA-2719315 sp902560065	85.312	195	331	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_002719315.1	s__GCA-2719315 sp002719315	85.1562	314	331	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_002723295.1	s__GCA-002723295 sp002723295	76.3575	52	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905381055.1	s__TMED220 sp905381055	75.8378	76	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	75.7581	51	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514625.1	s__TMED220 sp902514625	75.6332	51	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711185.1	s__GCA-002723295 sp002711185	75.5784	52	331	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	98.54	98.54	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:36:29,533] [INFO] GTDB search result was written to OceanDNA-b7111/result_gtdb.tsv
[2023-03-17 04:36:29,533] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:36:29,533] [INFO] DFAST_QC result json was written to OceanDNA-b7111/dqc_result.json
[2023-03-17 04:36:29,533] [INFO] DFAST_QC completed!
[2023-03-17 04:36:29,534] [INFO] Total running time: 0h0m54s