[2023-03-18 00:37:44,627] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:37:44,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:37:44,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference
[2023-03-18 00:37:45,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:37:45,724] [INFO] Task started: Prodigal
[2023-03-18 00:37:45,724] [INFO] Running command: cat /var/lib/cwl/stgd0b719f2-26e0-4f0e-8abd-dfb59fd7f2a9/OceanDNA-b44480.fa | prodigal -d OceanDNA-b44480/cds.fna -a OceanDNA-b44480/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:37:51,820] [INFO] Task succeeded: Prodigal
[2023-03-18 00:37:51,821] [INFO] Task started: HMMsearch
[2023-03-18 00:37:51,821] [INFO] Running command: hmmsearch --tblout OceanDNA-b44480/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference/reference_markers.hmm OceanDNA-b44480/protein.faa > /dev/null
[2023-03-18 00:37:51,982] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:37:51,983] [INFO] Found 6/6 markers.
[2023-03-18 00:37:51,994] [INFO] Query marker FASTA was written to OceanDNA-b44480/markers.fasta
[2023-03-18 00:37:51,995] [INFO] Task started: Blastn
[2023-03-18 00:37:51,996] [INFO] Running command: blastn -query OceanDNA-b44480/markers.fasta -db /var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference/reference_markers.fasta -out OceanDNA-b44480/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:37:52,525] [INFO] Task succeeded: Blastn
[2023-03-18 00:37:52,526] [INFO] Selected 23 target genomes.
[2023-03-18 00:37:52,526] [INFO] Target genome list was writen to OceanDNA-b44480/target_genomes.txt
[2023-03-18 00:37:52,536] [INFO] Task started: fastANI
[2023-03-18 00:37:52,536] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0b719f2-26e0-4f0e-8abd-dfb59fd7f2a9/OceanDNA-b44480.fa --refList OceanDNA-b44480/target_genomes.txt --output OceanDNA-b44480/fastani_result.tsv --threads 1
[2023-03-18 00:38:05,396] [INFO] Task succeeded: fastANI
[2023-03-18 00:38:05,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:38:05,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:38:05,396] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:38:05,396] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:38:05,396] [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 00:38:05,397] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44480/tc_result.tsv
[2023-03-18 00:38:05,397] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:38:05,397] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:38:05,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference/checkm_data
[2023-03-18 00:38:05,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:38:05,439] [INFO] Task started: CheckM
[2023-03-18 00:38:05,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44480/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44480/checkm_input OceanDNA-b44480/checkm_result
[2023-03-18 00:38:26,899] [INFO] Task succeeded: CheckM
[2023-03-18 00:38:26,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.36%
Contamintation: 5.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 00:38:26,902] [INFO] ===== Completeness check finished =====
[2023-03-18 00:38:26,902] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:38:26,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44480/markers.fasta)
[2023-03-18 00:38:26,903] [INFO] Task started: Blastn
[2023-03-18 00:38:26,904] [INFO] Running command: blastn -query OceanDNA-b44480/markers.fasta -db /var/lib/cwl/stg7ce58276-c6b9-421f-bcbc-b50318824272/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44480/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:38:27,746] [INFO] Task succeeded: Blastn
[2023-03-18 00:38:27,747] [INFO] Selected 23 target genomes.
[2023-03-18 00:38:27,748] [INFO] Target genome list was writen to OceanDNA-b44480/target_genomes_gtdb.txt
[2023-03-18 00:38:27,767] [INFO] Task started: fastANI
[2023-03-18 00:38:27,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0b719f2-26e0-4f0e-8abd-dfb59fd7f2a9/OceanDNA-b44480.fa --refList OceanDNA-b44480/target_genomes_gtdb.txt --output OceanDNA-b44480/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:38:34,363] [INFO] Task succeeded: fastANI
[2023-03-18 00:38:34,367] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:38:34,367] [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_902517795.1	s__SP4260 sp902517795	94.2545	234	361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	99.80	99.80	0.68	0.68	2	-
GCA_002728725.1	s__SP4260 sp002728725	92.6454	229	361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715745.1	s__SP4260 sp002715745	90.2108	262	361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	97.07	97.07	0.87	0.87	2	-
GCA_003331585.1	s__SP4260 sp003331585	77.7313	66	361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:38:34,368] [INFO] GTDB search result was written to OceanDNA-b44480/result_gtdb.tsv
[2023-03-18 00:38:34,368] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:38:34,368] [INFO] DFAST_QC result json was written to OceanDNA-b44480/dqc_result.json
[2023-03-18 00:38:34,368] [INFO] DFAST_QC completed!
[2023-03-18 00:38:34,369] [INFO] Total running time: 0h0m50s