[2023-03-15 15:55:16,229] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,234] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,234] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,913] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,913] [INFO] Running command: cat /var/lib/cwl/stg53433a70-4c4d-49e2-ba3b-e1763855c112/OceanDNA-b21261.fa | prodigal -d OceanDNA-b21261/cds.fna -a OceanDNA-b21261/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:24,692] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:24,693] [INFO] Task started: HMMsearch
[2023-03-15 15:55:24,693] [INFO] Running command: hmmsearch --tblout OceanDNA-b21261/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference/reference_markers.hmm OceanDNA-b21261/protein.faa > /dev/null
[2023-03-15 15:55:24,899] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:24,899] [INFO] Found 6/6 markers.
[2023-03-15 15:55:24,912] [INFO] Query marker FASTA was written to OceanDNA-b21261/markers.fasta
[2023-03-15 15:55:24,912] [INFO] Task started: Blastn
[2023-03-15 15:55:24,912] [INFO] Running command: blastn -query OceanDNA-b21261/markers.fasta -db /var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference/reference_markers.fasta -out OceanDNA-b21261/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:25,470] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:25,471] [INFO] Selected 18 target genomes.
[2023-03-15 15:55:25,471] [INFO] Target genome list was writen to OceanDNA-b21261/target_genomes.txt
[2023-03-15 15:55:25,497] [INFO] Task started: fastANI
[2023-03-15 15:55:25,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg53433a70-4c4d-49e2-ba3b-e1763855c112/OceanDNA-b21261.fa --refList OceanDNA-b21261/target_genomes.txt --output OceanDNA-b21261/fastani_result.tsv --threads 1
[2023-03-15 15:55:33,431] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:33,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:33,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:33,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:33,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:33,432] [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 15:55:33,432] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21261/tc_result.tsv
[2023-03-15 15:55:33,433] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:33,433] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:33,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference/checkm_data
[2023-03-15 15:55:33,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:33,439] [INFO] Task started: CheckM
[2023-03-15 15:55:33,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21261/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21261/checkm_input OceanDNA-b21261/checkm_result
[2023-03-15 15:55:55,661] [INFO] Task succeeded: CheckM
[2023-03-15 15:55:55,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:55:55,663] [INFO] ===== Completeness check finished =====
[2023-03-15 15:55:55,664] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:55:55,664] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21261/markers.fasta)
[2023-03-15 15:55:55,665] [INFO] Task started: Blastn
[2023-03-15 15:55:55,665] [INFO] Running command: blastn -query OceanDNA-b21261/markers.fasta -db /var/lib/cwl/stgaa6fd5ad-146f-4763-8270-720bf33360e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21261/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:56,552] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:56,553] [INFO] Selected 16 target genomes.
[2023-03-15 15:55:56,553] [INFO] Target genome list was writen to OceanDNA-b21261/target_genomes_gtdb.txt
[2023-03-15 15:55:56,587] [INFO] Task started: fastANI
[2023-03-15 15:55:56,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg53433a70-4c4d-49e2-ba3b-e1763855c112/OceanDNA-b21261.fa --refList OceanDNA-b21261/target_genomes_gtdb.txt --output OceanDNA-b21261/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:02,131] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:02,135] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:02,135] [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_000372225.1	s__Nitromaritima sp000372225	93.6686	271	374	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647025.1	s__Nitromaritima sp018647025	82.1839	209	374	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	98.38	98.13	0.71	0.67	3	-
GCA_018697205.1	s__Nitromaritima sp018697205	80.1106	245	374	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	-
GCA_905182935.1	s__Nitromaritima sp905182935	77.2997	89	374	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002731985.1	s__Nitromaritima sp002731985	76.5851	56	374	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.05	98.90	0.81	0.77	3	-
GCA_003451695.1	s__Nitromaritima sp003451695	76.5783	51	374	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	97.02	97.02	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:02,136] [INFO] GTDB search result was written to OceanDNA-b21261/result_gtdb.tsv
[2023-03-15 15:56:02,136] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:02,136] [INFO] DFAST_QC result json was written to OceanDNA-b21261/dqc_result.json
[2023-03-15 15:56:02,137] [INFO] DFAST_QC completed!
[2023-03-15 15:56:02,137] [INFO] Total running time: 0h0m46s