[2023-03-17 00:27:15,238] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:27:15,239] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:27:15,239] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference
[2023-03-17 00:27:16,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:27:16,353] [INFO] Task started: Prodigal
[2023-03-17 00:27:16,353] [INFO] Running command: cat /var/lib/cwl/stg54e24b1b-4d47-4147-bcdd-b5388aaeb6ff/OceanDNA-b21299.fa | prodigal -d OceanDNA-b21299/cds.fna -a OceanDNA-b21299/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:27:25,677] [INFO] Task succeeded: Prodigal
[2023-03-17 00:27:25,677] [INFO] Task started: HMMsearch
[2023-03-17 00:27:25,677] [INFO] Running command: hmmsearch --tblout OceanDNA-b21299/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference/reference_markers.hmm OceanDNA-b21299/protein.faa > /dev/null
[2023-03-17 00:27:25,868] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:27:25,869] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg54e24b1b-4d47-4147-bcdd-b5388aaeb6ff/OceanDNA-b21299.fa]
[2023-03-17 00:27:25,883] [INFO] Query marker FASTA was written to OceanDNA-b21299/markers.fasta
[2023-03-17 00:27:25,884] [INFO] Task started: Blastn
[2023-03-17 00:27:25,884] [INFO] Running command: blastn -query OceanDNA-b21299/markers.fasta -db /var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference/reference_markers.fasta -out OceanDNA-b21299/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:27:26,422] [INFO] Task succeeded: Blastn
[2023-03-17 00:27:26,422] [INFO] Selected 22 target genomes.
[2023-03-17 00:27:26,423] [INFO] Target genome list was writen to OceanDNA-b21299/target_genomes.txt
[2023-03-17 00:27:26,434] [INFO] Task started: fastANI
[2023-03-17 00:27:26,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg54e24b1b-4d47-4147-bcdd-b5388aaeb6ff/OceanDNA-b21299.fa --refList OceanDNA-b21299/target_genomes.txt --output OceanDNA-b21299/fastani_result.tsv --threads 1
[2023-03-17 00:30:23,380] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:23,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:30:23,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:30:23,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:30:23,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:30:23,381] [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
--------------------------------------------------------------------------------
[2023-03-17 00:30:23,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21299/tc_result.tsv
[2023-03-17 00:30:23,381] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:30:23,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:30:23,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference/checkm_data
[2023-03-17 00:30:23,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:30:23,387] [INFO] Task started: CheckM
[2023-03-17 00:30:23,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21299/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21299/checkm_input OceanDNA-b21299/checkm_result
[2023-03-17 00:30:51,314] [INFO] Task succeeded: CheckM
[2023-03-17 00:30:51,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:30:51,317] [INFO] ===== Completeness check finished =====
[2023-03-17 00:30:51,317] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:30:51,317] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21299/markers.fasta)
[2023-03-17 00:30:51,318] [INFO] Task started: Blastn
[2023-03-17 00:30:51,318] [INFO] Running command: blastn -query OceanDNA-b21299/markers.fasta -db /var/lib/cwl/stgf0dba985-a175-4988-99ca-843391c1fd30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21299/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:30:52,346] [INFO] Task succeeded: Blastn
[2023-03-17 00:30:52,347] [INFO] Selected 19 target genomes.
[2023-03-17 00:30:52,347] [INFO] Target genome list was writen to OceanDNA-b21299/target_genomes_gtdb.txt
[2023-03-17 00:30:52,437] [INFO] Task started: fastANI
[2023-03-17 00:30:52,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg54e24b1b-4d47-4147-bcdd-b5388aaeb6ff/OceanDNA-b21299.fa --refList OceanDNA-b21299/target_genomes_gtdb.txt --output OceanDNA-b21299/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:30:59,801] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:59,804] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:30:59,804] [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_018697205.1	s__Nitromaritima sp018697205	99.6942	512	604	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	99.64	99.64	0.83	0.83	2	conclusive
GCA_000372225.1	s__Nitromaritima sp000372225	80.3848	301	604	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	79.3748	216	604	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	98.38	98.13	0.71	0.67	3	-
GCA_905182935.1	s__Nitromaritima sp905182935	77.5464	117	604	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitromaritima	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:30:59,805] [INFO] GTDB search result was written to OceanDNA-b21299/result_gtdb.tsv
[2023-03-17 00:30:59,805] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:30:59,805] [INFO] DFAST_QC result json was written to OceanDNA-b21299/dqc_result.json
[2023-03-17 00:30:59,805] [INFO] DFAST_QC completed!
[2023-03-17 00:30:59,805] [INFO] Total running time: 0h3m45s