[2023-03-18 01:26:26,376] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,377] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference
[2023-03-18 01:26:27,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,579] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,579] [INFO] Running command: cat /var/lib/cwl/stg5f7fbacc-6e39-44d0-8107-df8c8b5c4a2d/OceanDNA-b44724.fa | prodigal -d OceanDNA-b44724/cds.fna -a OceanDNA-b44724/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:36,536] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:36,536] [INFO] Task started: HMMsearch
[2023-03-18 01:26:36,536] [INFO] Running command: hmmsearch --tblout OceanDNA-b44724/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference/reference_markers.hmm OceanDNA-b44724/protein.faa > /dev/null
[2023-03-18 01:26:36,717] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:36,717] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5f7fbacc-6e39-44d0-8107-df8c8b5c4a2d/OceanDNA-b44724.fa]
[2023-03-18 01:26:36,728] [INFO] Query marker FASTA was written to OceanDNA-b44724/markers.fasta
[2023-03-18 01:26:36,729] [INFO] Task started: Blastn
[2023-03-18 01:26:36,729] [INFO] Running command: blastn -query OceanDNA-b44724/markers.fasta -db /var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference/reference_markers.fasta -out OceanDNA-b44724/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:37,246] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:37,247] [INFO] Selected 11 target genomes.
[2023-03-18 01:26:37,248] [INFO] Target genome list was writen to OceanDNA-b44724/target_genomes.txt
[2023-03-18 01:26:37,256] [INFO] Task started: fastANI
[2023-03-18 01:26:37,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f7fbacc-6e39-44d0-8107-df8c8b5c4a2d/OceanDNA-b44724.fa --refList OceanDNA-b44724/target_genomes.txt --output OceanDNA-b44724/fastani_result.tsv --threads 1
[2023-03-18 01:26:42,220] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:42,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:42,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:42,221] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:42,221] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:42,221] [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
--------------------------------------------------------------------------------
[2023-03-18 01:26:42,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44724/tc_result.tsv
[2023-03-18 01:26:42,222] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:42,222] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:42,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference/checkm_data
[2023-03-18 01:26:42,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:42,228] [INFO] Task started: CheckM
[2023-03-18 01:26:42,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44724/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44724/checkm_input OceanDNA-b44724/checkm_result
[2023-03-18 01:27:10,512] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:10,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.24%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:10,514] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:10,515] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:10,515] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44724/markers.fasta)
[2023-03-18 01:27:10,516] [INFO] Task started: Blastn
[2023-03-18 01:27:10,516] [INFO] Running command: blastn -query OceanDNA-b44724/markers.fasta -db /var/lib/cwl/stg29fed710-3308-4f6f-b288-649ce65b7fd0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44724/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:11,214] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:11,215] [INFO] Selected 14 target genomes.
[2023-03-18 01:27:11,215] [INFO] Target genome list was writen to OceanDNA-b44724/target_genomes_gtdb.txt
[2023-03-18 01:27:11,243] [INFO] Task started: fastANI
[2023-03-18 01:27:11,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f7fbacc-6e39-44d0-8107-df8c8b5c4a2d/OceanDNA-b44724.fa --refList OceanDNA-b44724/target_genomes_gtdb.txt --output OceanDNA-b44724/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:16,772] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:16,776] [INFO] Found 4 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 01:27:16,776] [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_002716165.1	s__Arctic96AD-7 sp002716165	98.8528	248	438	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	inconclusive
GCA_902564345.1	s__Arctic96AD-7 sp902564345	96.2779	233	438	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	inconclusive
GCA_902562015.1	s__Arctic96AD-7 sp902562015	81.4078	207	438	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_001627865.1	s__Arctic96AD-7 sp001627865	76.7505	148	438	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	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:16,777] [INFO] GTDB search result was written to OceanDNA-b44724/result_gtdb.tsv
[2023-03-18 01:27:16,777] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:16,778] [INFO] DFAST_QC result json was written to OceanDNA-b44724/dqc_result.json
[2023-03-18 01:27:16,778] [INFO] DFAST_QC completed!
[2023-03-18 01:27:16,778] [INFO] Total running time: 0h0m50s