[2023-03-17 03:24:50,917] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,917] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,917] [INFO] DQC Reference Directory: /var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference
[2023-03-17 03:24:52,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,057] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,057] [INFO] Running command: cat /var/lib/cwl/stg7ba3b257-bb37-4fea-ad95-7ab301d05f35/OceanDNA-b29855.fa | prodigal -d OceanDNA-b29855/cds.fna -a OceanDNA-b29855/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:25:04,995] [INFO] Task succeeded: Prodigal
[2023-03-17 03:25:04,996] [INFO] Task started: HMMsearch
[2023-03-17 03:25:04,996] [INFO] Running command: hmmsearch --tblout OceanDNA-b29855/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference/reference_markers.hmm OceanDNA-b29855/protein.faa > /dev/null
[2023-03-17 03:25:05,177] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:25:05,178] [INFO] Found 6/6 markers.
[2023-03-17 03:25:05,193] [INFO] Query marker FASTA was written to OceanDNA-b29855/markers.fasta
[2023-03-17 03:25:05,194] [INFO] Task started: Blastn
[2023-03-17 03:25:05,194] [INFO] Running command: blastn -query OceanDNA-b29855/markers.fasta -db /var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference/reference_markers.fasta -out OceanDNA-b29855/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:05,720] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:05,721] [INFO] Selected 30 target genomes.
[2023-03-17 03:25:05,721] [INFO] Target genome list was writen to OceanDNA-b29855/target_genomes.txt
[2023-03-17 03:25:05,740] [INFO] Task started: fastANI
[2023-03-17 03:25:05,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ba3b257-bb37-4fea-ad95-7ab301d05f35/OceanDNA-b29855.fa --refList OceanDNA-b29855/target_genomes.txt --output OceanDNA-b29855/fastani_result.tsv --threads 1
[2023-03-17 03:25:21,291] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:21,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:21,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:21,295] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:21,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:25:21,295] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	77.2733	156	709	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:25:21,296] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29855/tc_result.tsv
[2023-03-17 03:25:21,299] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:21,299] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:21,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference/checkm_data
[2023-03-17 03:25:21,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:21,304] [INFO] Task started: CheckM
[2023-03-17 03:25:21,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29855/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29855/checkm_input OceanDNA-b29855/checkm_result
[2023-03-17 03:25:57,287] [INFO] Task succeeded: CheckM
[2023-03-17 03:25:57,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.47%
Contamintation: 6.77%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-17 03:25:57,298] [INFO] ===== Completeness check finished =====
[2023-03-17 03:25:57,298] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:25:57,298] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29855/markers.fasta)
[2023-03-17 03:25:57,299] [INFO] Task started: Blastn
[2023-03-17 03:25:57,299] [INFO] Running command: blastn -query OceanDNA-b29855/markers.fasta -db /var/lib/cwl/stga07d4c15-10db-4ba2-8675-c7bc8e8670ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29855/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:58,033] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:58,034] [INFO] Selected 18 target genomes.
[2023-03-17 03:25:58,034] [INFO] Target genome list was writen to OceanDNA-b29855/target_genomes_gtdb.txt
[2023-03-17 03:25:58,050] [INFO] Task started: fastANI
[2023-03-17 03:25:58,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ba3b257-bb37-4fea-ad95-7ab301d05f35/OceanDNA-b29855.fa --refList OceanDNA-b29855/target_genomes_gtdb.txt --output OceanDNA-b29855/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:26:07,162] [INFO] Task succeeded: fastANI
[2023-03-17 03:26:07,168] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:26:07,168] [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_000981705.1	s__Planktomarina sp000981705	99.2787	660	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	conclusive
GCA_905182535.1	s__Planktomarina sp905182535	92.8189	570	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.42	98.42	0.82	0.82	2	-
GCA_905182195.1	s__Planktomarina sp905182195	79.7199	340	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182455.1	s__Planktomarina sp905182455	79.6612	357	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181815.1	s__Planktomarina sp905181815	77.3227	149	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738435.1	s__Planktomarina temperata	77.2733	156	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	-
GCA_002683685.1	s__Planktomarina sp002683685	77.0861	112	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	-
GCA_016780825.1	s__Planktomarina sp016780825	76.7418	136	709	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:26:07,168] [INFO] GTDB search result was written to OceanDNA-b29855/result_gtdb.tsv
[2023-03-17 03:26:07,168] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:26:07,169] [INFO] DFAST_QC result json was written to OceanDNA-b29855/dqc_result.json
[2023-03-17 03:26:07,169] [INFO] DFAST_QC completed!
[2023-03-17 03:26:07,169] [INFO] Total running time: 0h1m16s