[2023-03-19 03:50:07,835] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,835] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,835] [INFO] DQC Reference Directory: /var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference
[2023-03-19 03:50:09,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,608] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,608] [INFO] Running command: cat /var/lib/cwl/stg9999e692-c056-4479-878f-f7cc48c6302b/OceanDNA-b8503.fa | prodigal -d OceanDNA-b8503/cds.fna -a OceanDNA-b8503/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:15,770] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:15,770] [INFO] Task started: HMMsearch
[2023-03-19 03:50:15,770] [INFO] Running command: hmmsearch --tblout OceanDNA-b8503/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference/reference_markers.hmm OceanDNA-b8503/protein.faa > /dev/null
[2023-03-19 03:50:15,994] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:15,995] [INFO] Found 6/6 markers.
[2023-03-19 03:50:16,004] [INFO] Query marker FASTA was written to OceanDNA-b8503/markers.fasta
[2023-03-19 03:50:16,005] [INFO] Task started: Blastn
[2023-03-19 03:50:16,005] [INFO] Running command: blastn -query OceanDNA-b8503/markers.fasta -db /var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference/reference_markers.fasta -out OceanDNA-b8503/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:16,577] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:16,578] [INFO] Selected 33 target genomes.
[2023-03-19 03:50:16,578] [INFO] Target genome list was writen to OceanDNA-b8503/target_genomes.txt
[2023-03-19 03:50:16,596] [INFO] Task started: fastANI
[2023-03-19 03:50:16,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg9999e692-c056-4479-878f-f7cc48c6302b/OceanDNA-b8503.fa --refList OceanDNA-b8503/target_genomes.txt --output OceanDNA-b8503/fastani_result.tsv --threads 1
[2023-03-19 03:50:34,409] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:34,409] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:34,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:34,410] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:34,410] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:34,410] [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 03:50:34,410] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8503/tc_result.tsv
[2023-03-19 03:50:34,410] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:34,410] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:34,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference/checkm_data
[2023-03-19 03:50:34,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:34,415] [INFO] Task started: CheckM
[2023-03-19 03:50:34,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8503/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8503/checkm_input OceanDNA-b8503/checkm_result
[2023-03-19 03:50:55,490] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:55,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:55,492] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:55,492] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:55,493] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8503/markers.fasta)
[2023-03-19 03:50:55,493] [INFO] Task started: Blastn
[2023-03-19 03:50:55,493] [INFO] Running command: blastn -query OceanDNA-b8503/markers.fasta -db /var/lib/cwl/stgac3696f0-ba5b-4b20-ab6d-62f524651847/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8503/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:56,442] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:56,442] [INFO] Selected 11 target genomes.
[2023-03-19 03:50:56,442] [INFO] Target genome list was writen to OceanDNA-b8503/target_genomes_gtdb.txt
[2023-03-19 03:50:56,456] [INFO] Task started: fastANI
[2023-03-19 03:50:56,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg9999e692-c056-4479-878f-f7cc48c6302b/OceanDNA-b8503.fa --refList OceanDNA-b8503/target_genomes_gtdb.txt --output OceanDNA-b8503/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:59,025] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:59,032] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:50:59,032] [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_902598525.1	s__MED-G11 sp902598525	97.0665	288	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.61	96.61	0.83	0.83	2	conclusive
GCA_902594745.1	s__MED-G11 sp902594745	85.0612	264	343	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_902583445.1	s__MED-G11 sp902583445	85.0404	205	343	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_016780245.1	s__MED-G11 sp016780245	85.0027	208	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	-
GCA_902577515.1	s__MED-G11 sp902577515	84.6352	229	343	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_902617285.1	s__MED-G11 sp902617285	84.4386	237	343	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_902560025.1	s__MED-G11 sp902560025	84.169	156	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856235.1	s__MED-G11 sp017856235	83.6577	252	343	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_905380995.1	s__MED-G11 sp905380995	77.7188	160	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509805.1	s__MED-G11 sp902509805	77.7006	101	343	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:59,032] [INFO] GTDB search result was written to OceanDNA-b8503/result_gtdb.tsv
[2023-03-19 03:50:59,032] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:59,033] [INFO] DFAST_QC result json was written to OceanDNA-b8503/dqc_result.json
[2023-03-19 03:50:59,033] [INFO] DFAST_QC completed!
[2023-03-19 03:50:59,033] [INFO] Total running time: 0h0m51s