[2023-03-16 03:23:48,507] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference
[2023-03-16 03:23:50,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,649] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,649] [INFO] Running command: cat /var/lib/cwl/stg7c2cc5e5-3817-4b7f-ac91-34c18cc7f22f/OceanDNA-b27155.fa | prodigal -d OceanDNA-b27155/cds.fna -a OceanDNA-b27155/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:56,281] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:56,282] [INFO] Task started: HMMsearch
[2023-03-16 03:23:56,282] [INFO] Running command: hmmsearch --tblout OceanDNA-b27155/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference/reference_markers.hmm OceanDNA-b27155/protein.faa > /dev/null
[2023-03-16 03:23:56,443] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:56,443] [INFO] Found 6/6 markers.
[2023-03-16 03:23:56,453] [INFO] Query marker FASTA was written to OceanDNA-b27155/markers.fasta
[2023-03-16 03:23:56,453] [INFO] Task started: Blastn
[2023-03-16 03:23:56,453] [INFO] Running command: blastn -query OceanDNA-b27155/markers.fasta -db /var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference/reference_markers.fasta -out OceanDNA-b27155/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:57,001] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:57,001] [INFO] Selected 17 target genomes.
[2023-03-16 03:23:57,002] [INFO] Target genome list was writen to OceanDNA-b27155/target_genomes.txt
[2023-03-16 03:23:57,011] [INFO] Task started: fastANI
[2023-03-16 03:23:57,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2cc5e5-3817-4b7f-ac91-34c18cc7f22f/OceanDNA-b27155.fa --refList OceanDNA-b27155/target_genomes.txt --output OceanDNA-b27155/fastani_result.tsv --threads 1
[2023-03-16 03:24:04,525] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:04,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:04,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:04,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:04,526] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:04,526] [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
--------------------------------------------------------------------------------
[2023-03-16 03:24:04,527] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27155/tc_result.tsv
[2023-03-16 03:24:04,527] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:04,527] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:04,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference/checkm_data
[2023-03-16 03:24:04,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:04,532] [INFO] Task started: CheckM
[2023-03-16 03:24:04,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27155/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27155/checkm_input OceanDNA-b27155/checkm_result
[2023-03-16 03:24:24,464] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:24,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.49%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:24,466] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:24,467] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:24,467] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27155/markers.fasta)
[2023-03-16 03:24:24,467] [INFO] Task started: Blastn
[2023-03-16 03:24:24,467] [INFO] Running command: blastn -query OceanDNA-b27155/markers.fasta -db /var/lib/cwl/stgfce378dc-f99b-40e2-a48c-b8176875a46a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27155/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:25,404] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:25,405] [INFO] Selected 18 target genomes.
[2023-03-16 03:24:25,405] [INFO] Target genome list was writen to OceanDNA-b27155/target_genomes_gtdb.txt
[2023-03-16 03:24:26,043] [INFO] Task started: fastANI
[2023-03-16 03:24:26,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c2cc5e5-3817-4b7f-ac91-34c18cc7f22f/OceanDNA-b27155.fa --refList OceanDNA-b27155/target_genomes_gtdb.txt --output OceanDNA-b27155/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:29,887] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:29,894] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:24:29,894] [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_002704345.1	s__MED-G09 sp002704345	80.2627	226	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.20	99.20	0.77	0.77	2	-
GCA_018658685.1	s__MED-G09 sp018658685	80.2169	205	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182015.1	s__MED-G09 sp905182015	79.5113	226	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278145.1	s__MED-G09 sp003278145	77.3801	143	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	98.26	96.25	0.89	0.83	4	-
GCA_003279705.1	s__MED-G09 sp003279705	77.3281	115	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	99.31	98.62	0.86	0.72	3	-
GCA_002170885.2	s__MED-G09 sp002170885	77.1054	64	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683015.1	s__MED-G09 sp002683015	77.0426	76	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723035.1	s__MED-G09 sp002723035	76.7751	73	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537725.1	s__MED-G09 sp902537725	76.7652	93	367	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__MED-G09;g__MED-G09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:29,894] [INFO] GTDB search result was written to OceanDNA-b27155/result_gtdb.tsv
[2023-03-16 03:24:29,894] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:29,895] [INFO] DFAST_QC result json was written to OceanDNA-b27155/dqc_result.json
[2023-03-16 03:24:29,895] [INFO] DFAST_QC completed!
[2023-03-16 03:24:29,895] [INFO] Total running time: 0h0m41s