[2023-03-17 23:08:31,946] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,949] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference
[2023-03-17 23:08:33,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,092] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,092] [INFO] Running command: cat /var/lib/cwl/stga0a9f5f2-48fc-4360-aede-4fad27113e83/OceanDNA-b28584.fa | prodigal -d OceanDNA-b28584/cds.fna -a OceanDNA-b28584/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:40,024] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:40,025] [INFO] Task started: HMMsearch
[2023-03-17 23:08:40,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b28584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference/reference_markers.hmm OceanDNA-b28584/protein.faa > /dev/null
[2023-03-17 23:08:40,190] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:40,190] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga0a9f5f2-48fc-4360-aede-4fad27113e83/OceanDNA-b28584.fa]
[2023-03-17 23:08:40,206] [INFO] Query marker FASTA was written to OceanDNA-b28584/markers.fasta
[2023-03-17 23:08:40,207] [INFO] Task started: Blastn
[2023-03-17 23:08:40,207] [INFO] Running command: blastn -query OceanDNA-b28584/markers.fasta -db /var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference/reference_markers.fasta -out OceanDNA-b28584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:40,767] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:40,770] [INFO] Selected 22 target genomes.
[2023-03-17 23:08:40,770] [INFO] Target genome list was writen to OceanDNA-b28584/target_genomes.txt
[2023-03-17 23:08:40,780] [INFO] Task started: fastANI
[2023-03-17 23:08:40,780] [INFO] Running command: fastANI --query /var/lib/cwl/stga0a9f5f2-48fc-4360-aede-4fad27113e83/OceanDNA-b28584.fa --refList OceanDNA-b28584/target_genomes.txt --output OceanDNA-b28584/fastani_result.tsv --threads 1
[2023-03-17 23:08:53,179] [INFO] Task succeeded: fastANI
[2023-03-17 23:08:53,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:08:53,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:08:53,180] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:08:53,180] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:08:53,180] [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 23:08:53,182] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28584/tc_result.tsv
[2023-03-17 23:08:53,183] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:08:53,183] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:08:53,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference/checkm_data
[2023-03-17 23:08:53,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:08:53,257] [INFO] Task started: CheckM
[2023-03-17 23:08:53,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28584/checkm_input OceanDNA-b28584/checkm_result
[2023-03-17 23:09:15,935] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:15,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.66%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:15,949] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:15,949] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:15,949] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28584/markers.fasta)
[2023-03-17 23:09:15,951] [INFO] Task started: Blastn
[2023-03-17 23:09:15,951] [INFO] Running command: blastn -query OceanDNA-b28584/markers.fasta -db /var/lib/cwl/stg3e5f7443-f402-4db0-b5c9-9c0745c2da58/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:16,774] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:16,777] [INFO] Selected 11 target genomes.
[2023-03-17 23:09:16,777] [INFO] Target genome list was writen to OceanDNA-b28584/target_genomes_gtdb.txt
[2023-03-17 23:09:16,785] [INFO] Task started: fastANI
[2023-03-17 23:09:16,785] [INFO] Running command: fastANI --query /var/lib/cwl/stga0a9f5f2-48fc-4360-aede-4fad27113e83/OceanDNA-b28584.fa --refList OceanDNA-b28584/target_genomes_gtdb.txt --output OceanDNA-b28584/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:22,231] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:22,234] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:09:22,234] [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_000472185.1	s__HIMB11 sp000472185	93.7392	208	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852835.1	s__HIMB11 sp003486095	91.8235	189	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	98.02	97.17	0.82	0.75	18	-
GCA_018222665.1	s__HIMB11 sp018222665	91.051	162	215	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:22,236] [INFO] GTDB search result was written to OceanDNA-b28584/result_gtdb.tsv
[2023-03-17 23:09:22,236] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:22,238] [INFO] DFAST_QC result json was written to OceanDNA-b28584/dqc_result.json
[2023-03-17 23:09:22,238] [INFO] DFAST_QC completed!
[2023-03-17 23:09:22,238] [INFO] Total running time: 0h0m50s