[2023-03-15 17:46:31,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,636] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference
[2023-03-15 17:46:32,772] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,773] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,773] [INFO] Running command: cat /var/lib/cwl/stgc039b67d-5e0e-422d-87f6-84e77d975293/OceanDNA-b44762.fa | prodigal -d OceanDNA-b44762/cds.fna -a OceanDNA-b44762/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:47,385] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:47,385] [INFO] Task started: HMMsearch
[2023-03-15 17:46:47,385] [INFO] Running command: hmmsearch --tblout OceanDNA-b44762/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference/reference_markers.hmm OceanDNA-b44762/protein.faa > /dev/null
[2023-03-15 17:46:47,620] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:47,621] [INFO] Found 6/6 markers.
[2023-03-15 17:46:47,654] [INFO] Query marker FASTA was written to OceanDNA-b44762/markers.fasta
[2023-03-15 17:46:47,654] [INFO] Task started: Blastn
[2023-03-15 17:46:47,654] [INFO] Running command: blastn -query OceanDNA-b44762/markers.fasta -db /var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference/reference_markers.fasta -out OceanDNA-b44762/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:48,215] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:48,223] [INFO] Selected 12 target genomes.
[2023-03-15 17:46:48,223] [INFO] Target genome list was writen to OceanDNA-b44762/target_genomes.txt
[2023-03-15 17:46:48,230] [INFO] Task started: fastANI
[2023-03-15 17:46:48,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgc039b67d-5e0e-422d-87f6-84e77d975293/OceanDNA-b44762.fa --refList OceanDNA-b44762/target_genomes.txt --output OceanDNA-b44762/fastani_result.tsv --threads 1
[2023-03-15 17:46:54,186] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:54,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:54,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:54,187] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:54,187] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:54,187] [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 17:46:54,190] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44762/tc_result.tsv
[2023-03-15 17:46:54,195] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:54,195] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:54,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference/checkm_data
[2023-03-15 17:46:54,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:54,203] [INFO] Task started: CheckM
[2023-03-15 17:46:54,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44762/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44762/checkm_input OceanDNA-b44762/checkm_result
[2023-03-15 17:47:34,384] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:34,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:34,392] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:34,392] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:34,392] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44762/markers.fasta)
[2023-03-15 17:47:34,394] [INFO] Task started: Blastn
[2023-03-15 17:47:34,394] [INFO] Running command: blastn -query OceanDNA-b44762/markers.fasta -db /var/lib/cwl/stg8ac13fd0-f215-4df1-a6cd-a9fe13f000d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44762/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:35,315] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:35,317] [INFO] Selected 8 target genomes.
[2023-03-15 17:47:35,318] [INFO] Target genome list was writen to OceanDNA-b44762/target_genomes_gtdb.txt
[2023-03-15 17:47:35,324] [INFO] Task started: fastANI
[2023-03-15 17:47:35,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgc039b67d-5e0e-422d-87f6-84e77d975293/OceanDNA-b44762.fa --refList OceanDNA-b44762/target_genomes_gtdb.txt --output OceanDNA-b44762/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:40,494] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:40,500] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:47:40,500] [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_014381795.1	s__Arctic96AD-7 sp014381795	98.8532	467	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018645085.1	s__Arctic96AD-7 sp018645085	90.9514	647	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	88.2202	619	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
GCA_004213175.1	s__Arctic96AD-7 sp002704555	82.138	500	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.39	96.63	0.73	0.69	4	-
GCA_016764995.1	s__Arctic96AD-7 sp016764995	81.2891	553	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964265.1	s__Arctic96AD-7 sp012964265	79.8477	389	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.25	98.98	0.81	0.73	8	-
GCA_014382365.1	s__Arctic96AD-7 sp014382365	78.6412	356	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.95	99.95	0.98	0.98	2	-
GCA_002082305.1	s__Arctic96AD-7 sp002082305	78.5237	373	862	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:40,502] [INFO] GTDB search result was written to OceanDNA-b44762/result_gtdb.tsv
[2023-03-15 17:47:40,503] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:40,506] [INFO] DFAST_QC result json was written to OceanDNA-b44762/dqc_result.json
[2023-03-15 17:47:40,506] [INFO] DFAST_QC completed!
[2023-03-15 17:47:40,506] [INFO] Total running time: 0h1m9s