[2023-03-16 23:42:36,498] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:42:36,498] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:42:36,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference
[2023-03-16 23:42:38,874] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:42:38,875] [INFO] Task started: Prodigal
[2023-03-16 23:42:38,875] [INFO] Running command: cat /var/lib/cwl/stg667d113f-4e56-48f7-96a2-f3cffe6dd142/OceanDNA-b44719.fa | prodigal -d OceanDNA-b44719/cds.fna -a OceanDNA-b44719/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:42:51,523] [INFO] Task succeeded: Prodigal
[2023-03-16 23:42:51,523] [INFO] Task started: HMMsearch
[2023-03-16 23:42:51,523] [INFO] Running command: hmmsearch --tblout OceanDNA-b44719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference/reference_markers.hmm OceanDNA-b44719/protein.faa > /dev/null
[2023-03-16 23:42:51,710] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:42:51,710] [INFO] Found 6/6 markers.
[2023-03-16 23:42:51,726] [INFO] Query marker FASTA was written to OceanDNA-b44719/markers.fasta
[2023-03-16 23:42:51,727] [INFO] Task started: Blastn
[2023-03-16 23:42:51,727] [INFO] Running command: blastn -query OceanDNA-b44719/markers.fasta -db /var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference/reference_markers.fasta -out OceanDNA-b44719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:42:52,280] [INFO] Task succeeded: Blastn
[2023-03-16 23:42:52,280] [INFO] Selected 15 target genomes.
[2023-03-16 23:42:52,281] [INFO] Target genome list was writen to OceanDNA-b44719/target_genomes.txt
[2023-03-16 23:42:52,318] [INFO] Task started: fastANI
[2023-03-16 23:42:52,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg667d113f-4e56-48f7-96a2-f3cffe6dd142/OceanDNA-b44719.fa --refList OceanDNA-b44719/target_genomes.txt --output OceanDNA-b44719/fastani_result.tsv --threads 1
[2023-03-16 23:42:59,647] [INFO] Task succeeded: fastANI
[2023-03-16 23:42:59,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:42:59,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:42:59,648] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:42:59,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:42:59,648] [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 23:42:59,648] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44719/tc_result.tsv
[2023-03-16 23:42:59,649] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:42:59,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:42:59,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference/checkm_data
[2023-03-16 23:42:59,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:42:59,765] [INFO] Task started: CheckM
[2023-03-16 23:42:59,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44719/checkm_input OceanDNA-b44719/checkm_result
[2023-03-16 23:43:37,315] [INFO] Task succeeded: CheckM
[2023-03-16 23:43:37,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.44%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:43:37,319] [INFO] ===== Completeness check finished =====
[2023-03-16 23:43:37,319] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:43:37,319] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44719/markers.fasta)
[2023-03-16 23:43:37,320] [INFO] Task started: Blastn
[2023-03-16 23:43:37,320] [INFO] Running command: blastn -query OceanDNA-b44719/markers.fasta -db /var/lib/cwl/stgd4895c8d-fef6-44b7-848a-ad65241f0d9d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:43:38,198] [INFO] Task succeeded: Blastn
[2023-03-16 23:43:38,199] [INFO] Selected 14 target genomes.
[2023-03-16 23:43:38,199] [INFO] Target genome list was writen to OceanDNA-b44719/target_genomes_gtdb.txt
[2023-03-16 23:43:38,210] [INFO] Task started: fastANI
[2023-03-16 23:43:38,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg667d113f-4e56-48f7-96a2-f3cffe6dd142/OceanDNA-b44719.fa --refList OceanDNA-b44719/target_genomes_gtdb.txt --output OceanDNA-b44719/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:43:44,821] [INFO] Task succeeded: fastANI
[2023-03-16 23:43:44,826] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:43:44,826] [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_902562015.1	s__Arctic96AD-7 sp902562015	85.0927	242	484	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_002716165.1	s__Arctic96AD-7 sp002716165	82.2065	203	484	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_902564345.1	s__Arctic96AD-7 sp902564345	81.9194	231	484	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.84	98.84	0.77	0.77	2	-
GCA_001627865.1	s__Arctic96AD-7 sp001627865	80.1489	340	484	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.71	99.45	0.95	0.94	9	-
GCA_002082305.1	s__Arctic96AD-7 sp002082305	76.4851	98	484	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	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	76.3112	62	484	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_018645085.1	s__Arctic96AD-7 sp018645085	76.1258	69	484	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_014382365.1	s__Arctic96AD-7 sp014382365	75.8893	56	484	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	-
--------------------------------------------------------------------------------
[2023-03-16 23:43:44,827] [INFO] GTDB search result was written to OceanDNA-b44719/result_gtdb.tsv
[2023-03-16 23:43:44,828] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:43:44,830] [INFO] DFAST_QC result json was written to OceanDNA-b44719/dqc_result.json
[2023-03-16 23:43:44,830] [INFO] DFAST_QC completed!
[2023-03-16 23:43:44,830] [INFO] Total running time: 0h1m8s