[2023-03-19 00:01:03,286] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,287] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference
[2023-03-19 00:01:04,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,535] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,535] [INFO] Running command: cat /var/lib/cwl/stgdd1e845e-81cd-475e-aaf7-d8d9e42baced/OceanDNA-b8531.fa | prodigal -d OceanDNA-b8531/cds.fna -a OceanDNA-b8531/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:09,701] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:09,702] [INFO] Task started: HMMsearch
[2023-03-19 00:01:09,702] [INFO] Running command: hmmsearch --tblout OceanDNA-b8531/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference/reference_markers.hmm OceanDNA-b8531/protein.faa > /dev/null
[2023-03-19 00:01:09,902] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:09,902] [INFO] Found 6/6 markers.
[2023-03-19 00:01:09,910] [INFO] Query marker FASTA was written to OceanDNA-b8531/markers.fasta
[2023-03-19 00:01:09,911] [INFO] Task started: Blastn
[2023-03-19 00:01:09,911] [INFO] Running command: blastn -query OceanDNA-b8531/markers.fasta -db /var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference/reference_markers.fasta -out OceanDNA-b8531/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:10,492] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:10,493] [INFO] Selected 29 target genomes.
[2023-03-19 00:01:10,493] [INFO] Target genome list was writen to OceanDNA-b8531/target_genomes.txt
[2023-03-19 00:01:10,507] [INFO] Task started: fastANI
[2023-03-19 00:01:10,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1e845e-81cd-475e-aaf7-d8d9e42baced/OceanDNA-b8531.fa --refList OceanDNA-b8531/target_genomes.txt --output OceanDNA-b8531/fastani_result.tsv --threads 1
[2023-03-19 00:01:24,601] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:24,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:24,602] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:24,602] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:24,602] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:24,602] [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
--------------------------------------------------------------------------------
[2023-03-19 00:01:24,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8531/tc_result.tsv
[2023-03-19 00:01:24,602] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:24,603] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:24,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference/checkm_data
[2023-03-19 00:01:24,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:24,608] [INFO] Task started: CheckM
[2023-03-19 00:01:24,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8531/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8531/checkm_input OceanDNA-b8531/checkm_result
[2023-03-19 00:01:43,778] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:43,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:43,883] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:43,884] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:43,884] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8531/markers.fasta)
[2023-03-19 00:01:43,884] [INFO] Task started: Blastn
[2023-03-19 00:01:43,884] [INFO] Running command: blastn -query OceanDNA-b8531/markers.fasta -db /var/lib/cwl/stg9446c47a-ce8a-4e97-aab6-0bd449e18865/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8531/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:44,822] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:44,823] [INFO] Selected 8 target genomes.
[2023-03-19 00:01:44,823] [INFO] Target genome list was writen to OceanDNA-b8531/target_genomes_gtdb.txt
[2023-03-19 00:01:44,835] [INFO] Task started: fastANI
[2023-03-19 00:01:44,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd1e845e-81cd-475e-aaf7-d8d9e42baced/OceanDNA-b8531.fa --refList OceanDNA-b8531/target_genomes_gtdb.txt --output OceanDNA-b8531/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:01:46,691] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:46,696] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-19 00:01:46,697] [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_902560025.1	s__MED-G11 sp902560025	97.1614	155	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_016780245.1	s__MED-G11 sp016780245	95.5907	200	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	inconclusive
GCA_902594745.1	s__MED-G11 sp902594745	94.952	253	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.86	97.86	0.89	0.89	2	-
GCA_902617285.1	s__MED-G11 sp902617285	92.4152	213	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.97	95.44	0.83	0.80	4	-
GCA_902583445.1	s__MED-G11 sp902583445	92.3532	187	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.54	95.81	0.70	0.67	3	-
GCA_902577515.1	s__MED-G11 sp902577515	91.2433	221	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.13	99.13	0.84	0.84	2	-
GCA_017856235.1	s__MED-G11 sp017856235	89.9437	241	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.25	98.96	0.92	0.89	4	-
GCA_902598525.1	s__MED-G11 sp902598525	86.2554	203	277	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.61	96.61	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:01:46,697] [INFO] GTDB search result was written to OceanDNA-b8531/result_gtdb.tsv
[2023-03-19 00:01:46,697] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:01:46,698] [INFO] DFAST_QC result json was written to OceanDNA-b8531/dqc_result.json
[2023-03-19 00:01:46,698] [INFO] DFAST_QC completed!
[2023-03-19 00:01:46,698] [INFO] Total running time: 0h0m43s