[2023-03-15 10:49:28,654] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,654] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference
[2023-03-15 10:49:29,804] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,804] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,804] [INFO] Running command: cat /var/lib/cwl/stga40e9d98-f73d-4780-8c27-4bba8f2dad40/OceanDNA-b1359.fa | prodigal -d OceanDNA-b1359/cds.fna -a OceanDNA-b1359/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:40,895] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:40,896] [INFO] Task started: HMMsearch
[2023-03-15 10:49:40,896] [INFO] Running command: hmmsearch --tblout OceanDNA-b1359/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference/reference_markers.hmm OceanDNA-b1359/protein.faa > /dev/null
[2023-03-15 10:49:41,068] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:41,069] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga40e9d98-f73d-4780-8c27-4bba8f2dad40/OceanDNA-b1359.fa]
[2023-03-15 10:49:41,085] [INFO] Query marker FASTA was written to OceanDNA-b1359/markers.fasta
[2023-03-15 10:49:41,085] [INFO] Task started: Blastn
[2023-03-15 10:49:41,085] [INFO] Running command: blastn -query OceanDNA-b1359/markers.fasta -db /var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference/reference_markers.fasta -out OceanDNA-b1359/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:41,576] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:41,577] [INFO] Selected 11 target genomes.
[2023-03-15 10:49:41,577] [INFO] Target genome list was writen to OceanDNA-b1359/target_genomes.txt
[2023-03-15 10:49:41,584] [INFO] Task started: fastANI
[2023-03-15 10:49:41,584] [INFO] Running command: fastANI --query /var/lib/cwl/stga40e9d98-f73d-4780-8c27-4bba8f2dad40/OceanDNA-b1359.fa --refList OceanDNA-b1359/target_genomes.txt --output OceanDNA-b1359/fastani_result.tsv --threads 1
[2023-03-15 10:49:47,550] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:47,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:47,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:47,552] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:47,552] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:47,552] [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 10:49:47,553] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1359/tc_result.tsv
[2023-03-15 10:49:47,553] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:47,553] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:47,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference/checkm_data
[2023-03-15 10:49:47,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:47,560] [INFO] Task started: CheckM
[2023-03-15 10:49:47,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1359/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1359/checkm_input OceanDNA-b1359/checkm_result
[2023-03-15 10:50:20,265] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:20,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:20,269] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:20,269] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:20,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1359/markers.fasta)
[2023-03-15 10:50:20,270] [INFO] Task started: Blastn
[2023-03-15 10:50:20,270] [INFO] Running command: blastn -query OceanDNA-b1359/markers.fasta -db /var/lib/cwl/stg9682ac14-84b4-41ef-81c7-523f506f0cf5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1359/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:20,930] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:20,931] [INFO] Selected 14 target genomes.
[2023-03-15 10:50:20,931] [INFO] Target genome list was writen to OceanDNA-b1359/target_genomes_gtdb.txt
[2023-03-15 10:50:20,947] [INFO] Task started: fastANI
[2023-03-15 10:50:20,947] [INFO] Running command: fastANI --query /var/lib/cwl/stga40e9d98-f73d-4780-8c27-4bba8f2dad40/OceanDNA-b1359.fa --refList OceanDNA-b1359/target_genomes_gtdb.txt --output OceanDNA-b1359/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:27,254] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:27,261] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:50:27,261] [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_004214275.1	s__MedAcidi-G3 sp004214275	87.4639	377	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713975.1	s__MedAcidi-G3 sp002713975	87.4379	380	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457435.1	s__MedAcidi-G3 sp002457435	87.116	457	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708935.1	s__MedAcidi-G3 sp002708935	86.8963	514	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722565.1	s__MedAcidi-G3 sp002722565	78.8895	303	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	96.30	96.09	0.94	0.94	4	-
GCA_003445455.1	s__MedAcidi-G3 sp003445455	78.5846	220	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	98.38	98.38	0.66	0.66	2	-
GCA_000817105.1	s__MedAcidi-G3 sp000817105	78.0854	230	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	99.01	98.43	0.87	0.75	11	-
GCA_002296525.1	s__UBA6944 sp002296525	77.6001	122	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	98.78	97.54	0.95	0.91	12	-
GCA_014239555.1	s__UBA2110 sp014239555	77.5355	97	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724355.1	s__UBA6944 sp002724355	76.9206	110	602	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA6944	95.0	98.32	97.68	0.80	0.76	5	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:27,261] [INFO] GTDB search result was written to OceanDNA-b1359/result_gtdb.tsv
[2023-03-15 10:50:27,262] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:27,263] [INFO] DFAST_QC result json was written to OceanDNA-b1359/dqc_result.json
[2023-03-15 10:50:27,263] [INFO] DFAST_QC completed!
[2023-03-15 10:50:27,263] [INFO] Total running time: 0h0m59s