[2023-03-17 05:01:06,757] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,758] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference
[2023-03-17 05:01:08,508] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:08,509] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,509] [INFO] Running command: cat /var/lib/cwl/stg1b57c4cb-373c-4956-9eca-64d56326af07/OceanDNA-b16246.fa | prodigal -d OceanDNA-b16246/cds.fna -a OceanDNA-b16246/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:21,278] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:21,278] [INFO] Task started: HMMsearch
[2023-03-17 05:01:21,278] [INFO] Running command: hmmsearch --tblout OceanDNA-b16246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference/reference_markers.hmm OceanDNA-b16246/protein.faa > /dev/null
[2023-03-17 05:01:21,422] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:21,422] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1b57c4cb-373c-4956-9eca-64d56326af07/OceanDNA-b16246.fa]
[2023-03-17 05:01:21,438] [INFO] Query marker FASTA was written to OceanDNA-b16246/markers.fasta
[2023-03-17 05:01:21,438] [INFO] Task started: Blastn
[2023-03-17 05:01:21,438] [INFO] Running command: blastn -query OceanDNA-b16246/markers.fasta -db /var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference/reference_markers.fasta -out OceanDNA-b16246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:21,884] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:21,884] [INFO] Selected 15 target genomes.
[2023-03-17 05:01:21,885] [INFO] Target genome list was writen to OceanDNA-b16246/target_genomes.txt
[2023-03-17 05:01:21,894] [INFO] Task started: fastANI
[2023-03-17 05:01:21,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b57c4cb-373c-4956-9eca-64d56326af07/OceanDNA-b16246.fa --refList OceanDNA-b16246/target_genomes.txt --output OceanDNA-b16246/fastani_result.tsv --threads 1
[2023-03-17 05:01:30,097] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:30,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:30,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:30,100] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:30,100] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:01:30,100] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	78.0664	111	314	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:01:30,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16246/tc_result.tsv
[2023-03-17 05:01:30,101] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:30,101] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:30,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference/checkm_data
[2023-03-17 05:01:30,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:30,158] [INFO] Task started: CheckM
[2023-03-17 05:01:30,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16246/checkm_input OceanDNA-b16246/checkm_result
[2023-03-17 05:02:06,439] [INFO] Task succeeded: CheckM
[2023-03-17 05:02:06,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 10.88%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 05:02:06,442] [INFO] ===== Completeness check finished =====
[2023-03-17 05:02:06,443] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:02:06,443] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16246/markers.fasta)
[2023-03-17 05:02:06,443] [INFO] Task started: Blastn
[2023-03-17 05:02:06,443] [INFO] Running command: blastn -query OceanDNA-b16246/markers.fasta -db /var/lib/cwl/stg9e832f6e-7912-47e2-b505-db6ca8ca6125/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:02:06,943] [INFO] Task succeeded: Blastn
[2023-03-17 05:02:06,944] [INFO] Selected 7 target genomes.
[2023-03-17 05:02:06,944] [INFO] Target genome list was writen to OceanDNA-b16246/target_genomes_gtdb.txt
[2023-03-17 05:02:07,027] [INFO] Task started: fastANI
[2023-03-17 05:02:07,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b57c4cb-373c-4956-9eca-64d56326af07/OceanDNA-b16246.fa --refList OceanDNA-b16246/target_genomes_gtdb.txt --output OceanDNA-b16246/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:02:10,332] [INFO] Task succeeded: fastANI
[2023-03-17 05:02:10,338] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 05:02:10,338] [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
GCF_015840335.1	s__Cyanobium_A sp015840335	96.149	300	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_013205255.1	s__Cyanobium_A sp013205255	95.7609	211	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_002252665.1	s__Cyanobium_A sp002252665	84.4386	277	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882385.1	s__Cyanobium_A sp016882385	84.2816	227	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697415.1	s__Cyanobium_A sp014697415	84.2024	283	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011885.1	s__Cyanobium_A usitatum	82.8579	265	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252675.1	s__Cyanobium sp002252675	80.8671	230	314	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
--------------------------------------------------------------------------------
[2023-03-17 05:02:10,338] [INFO] GTDB search result was written to OceanDNA-b16246/result_gtdb.tsv
[2023-03-17 05:02:10,338] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:02:10,339] [INFO] DFAST_QC result json was written to OceanDNA-b16246/dqc_result.json
[2023-03-17 05:02:10,339] [INFO] DFAST_QC completed!
[2023-03-17 05:02:10,339] [INFO] Total running time: 0h1m4s