[2023-03-15 10:52:57,300] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,300] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,300] [INFO] DQC Reference Directory: /var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference
[2023-03-15 10:52:58,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,864] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,864] [INFO] Running command: cat /var/lib/cwl/stg70b8cc2f-16ad-4131-9cc6-d1893ec735b5/OceanDNA-b16317.fa | prodigal -d OceanDNA-b16317/cds.fna -a OceanDNA-b16317/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:01,793] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:01,793] [INFO] Task started: HMMsearch
[2023-03-15 10:53:01,793] [INFO] Running command: hmmsearch --tblout OceanDNA-b16317/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference/reference_markers.hmm OceanDNA-b16317/protein.faa > /dev/null
[2023-03-15 10:53:01,964] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:01,965] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg70b8cc2f-16ad-4131-9cc6-d1893ec735b5/OceanDNA-b16317.fa]
[2023-03-15 10:53:01,971] [INFO] Query marker FASTA was written to OceanDNA-b16317/markers.fasta
[2023-03-15 10:53:01,973] [INFO] Task started: Blastn
[2023-03-15 10:53:01,973] [INFO] Running command: blastn -query OceanDNA-b16317/markers.fasta -db /var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference/reference_markers.fasta -out OceanDNA-b16317/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:05,062] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:05,063] [INFO] Selected 13 target genomes.
[2023-03-15 10:53:05,063] [INFO] Target genome list was writen to OceanDNA-b16317/target_genomes.txt
[2023-03-15 10:53:05,072] [INFO] Task started: fastANI
[2023-03-15 10:53:05,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg70b8cc2f-16ad-4131-9cc6-d1893ec735b5/OceanDNA-b16317.fa --refList OceanDNA-b16317/target_genomes.txt --output OceanDNA-b16317/fastani_result.tsv --threads 1
[2023-03-15 10:53:10,720] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:10,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:10,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:10,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:10,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:53:10,721] [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 10:53:10,721] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16317/tc_result.tsv
[2023-03-15 10:53:10,721] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:10,721] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:10,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference/checkm_data
[2023-03-15 10:53:10,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:10,791] [INFO] Task started: CheckM
[2023-03-15 10:53:10,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16317/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16317/checkm_input OceanDNA-b16317/checkm_result
[2023-03-15 10:53:25,726] [INFO] Task succeeded: CheckM
[2023-03-15 10:53:25,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.21%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:53:25,727] [INFO] ===== Completeness check finished =====
[2023-03-15 10:53:25,728] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:53:25,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16317/markers.fasta)
[2023-03-15 10:53:25,729] [INFO] Task started: Blastn
[2023-03-15 10:53:25,730] [INFO] Running command: blastn -query OceanDNA-b16317/markers.fasta -db /var/lib/cwl/stgdae6482a-79b0-4510-b8c2-d558c2c334e8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16317/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:26,356] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:26,357] [INFO] Selected 12 target genomes.
[2023-03-15 10:53:26,357] [INFO] Target genome list was writen to OceanDNA-b16317/target_genomes_gtdb.txt
[2023-03-15 10:53:26,371] [INFO] Task started: fastANI
[2023-03-15 10:53:26,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg70b8cc2f-16ad-4131-9cc6-d1893ec735b5/OceanDNA-b16317.fa --refList OceanDNA-b16317/target_genomes_gtdb.txt --output OceanDNA-b16317/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:53:28,659] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:28,667] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 10:53:28,667] [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_003210285.1	s__Prochlorococcus_A sp003210285	98.2684	91	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	97.88	97.67	0.88	0.87	3	inconclusive
GCA_003210275.1	s__Prochlorococcus_A sp003210275	96.4482	69	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_003210235.1	s__Prochlorococcus_A sp003210235	94.9911	55	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210655.1	s__Prochlorococcus_A sp003210655	93.9646	61	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279855.1	s__Prochlorococcus_A sp003279855	93.3388	94	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211135.1	s__Prochlorococcus_A sp003211135	93.0848	81	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210915.1	s__Prochlorococcus_A sp003210915	92.9854	78	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211655.1	s__Prochlorococcus_A sp003211655	92.8916	61	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210825.1	s__Prochlorococcus_A sp003210825	92.6986	65	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003208885.1	s__Prochlorococcus_A sp003208885	91.9118	68	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003210895.1	s__Prochlorococcus_A sp003210895	89.6942	80	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279875.1	s__Prochlorococcus_A sp003279875	88.1559	80	94	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:53:28,667] [INFO] GTDB search result was written to OceanDNA-b16317/result_gtdb.tsv
[2023-03-15 10:53:28,667] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:53:28,668] [INFO] DFAST_QC result json was written to OceanDNA-b16317/dqc_result.json
[2023-03-15 10:53:28,668] [INFO] DFAST_QC completed!
[2023-03-15 10:53:28,669] [INFO] Total running time: 0h0m31s