[2023-03-15 15:55:16,219] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,912] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,912] [INFO] Running command: cat /var/lib/cwl/stg64793378-fff6-494c-807d-0675316f0681/OceanDNA-b5053.fa | prodigal -d OceanDNA-b5053/cds.fna -a OceanDNA-b5053/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:23,712] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:23,712] [INFO] Task started: HMMsearch
[2023-03-15 15:55:23,712] [INFO] Running command: hmmsearch --tblout OceanDNA-b5053/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference/reference_markers.hmm OceanDNA-b5053/protein.faa > /dev/null
[2023-03-15 15:55:23,868] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:23,869] [INFO] Found 6/6 markers.
[2023-03-15 15:55:23,879] [INFO] Query marker FASTA was written to OceanDNA-b5053/markers.fasta
[2023-03-15 15:55:23,880] [INFO] Task started: Blastn
[2023-03-15 15:55:23,880] [INFO] Running command: blastn -query OceanDNA-b5053/markers.fasta -db /var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference/reference_markers.fasta -out OceanDNA-b5053/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:24,433] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:24,434] [INFO] Selected 32 target genomes.
[2023-03-15 15:55:24,434] [INFO] Target genome list was writen to OceanDNA-b5053/target_genomes.txt
[2023-03-15 15:55:24,452] [INFO] Task started: fastANI
[2023-03-15 15:55:24,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg64793378-fff6-494c-807d-0675316f0681/OceanDNA-b5053.fa --refList OceanDNA-b5053/target_genomes.txt --output OceanDNA-b5053/fastani_result.tsv --threads 1
[2023-03-15 15:55:42,322] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:42,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:42,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:42,323] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:42,323] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:42,323] [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
--------------------------------------------------------------------------------
[2023-03-15 15:55:42,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5053/tc_result.tsv
[2023-03-15 15:55:42,323] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:42,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:42,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference/checkm_data
[2023-03-15 15:55:42,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:42,329] [INFO] Task started: CheckM
[2023-03-15 15:55:42,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5053/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5053/checkm_input OceanDNA-b5053/checkm_result
[2023-03-15 15:56:02,973] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:02,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:02,975] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:02,975] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:02,975] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5053/markers.fasta)
[2023-03-15 15:56:02,975] [INFO] Task started: Blastn
[2023-03-15 15:56:02,975] [INFO] Running command: blastn -query OceanDNA-b5053/markers.fasta -db /var/lib/cwl/stg94722b78-54ab-469e-b9a0-a466b17ffbbd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5053/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:03,755] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:03,756] [INFO] Selected 10 target genomes.
[2023-03-15 15:56:03,756] [INFO] Target genome list was writen to OceanDNA-b5053/target_genomes_gtdb.txt
[2023-03-15 15:56:03,761] [INFO] Task started: fastANI
[2023-03-15 15:56:03,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg64793378-fff6-494c-807d-0675316f0681/OceanDNA-b5053.fa --refList OceanDNA-b5053/target_genomes_gtdb.txt --output OceanDNA-b5053/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:06,111] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:06,118] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:06,118] [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_014384505.1	s__UWMA-0277 sp014384505	94.8302	213	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	89.1214	196	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_905181635.1	s__UWMA-0277 sp905181635	89.0605	154	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182255.1	s__UWMA-0277 sp905182255	88.2158	131	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	81.6985	182	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	80.8542	182	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_012960805.1	s__UWMA-0277 sp012960805	80.518	182	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	80.151	169	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	80.1318	178	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612305.1	s__UWMA-0277 sp905612305	80.1065	143	263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:06,118] [INFO] GTDB search result was written to OceanDNA-b5053/result_gtdb.tsv
[2023-03-15 15:56:06,118] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:06,119] [INFO] DFAST_QC result json was written to OceanDNA-b5053/dqc_result.json
[2023-03-15 15:56:06,119] [INFO] DFAST_QC completed!
[2023-03-15 15:56:06,119] [INFO] Total running time: 0h0m50s