[2023-03-14 11:33:34,968] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference
[2023-03-14 11:33:36,243] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,243] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,243] [INFO] Running command: cat /var/lib/cwl/stgc415d3f2-da0f-4c94-87fe-d3d1c30df1c9/OceanDNA-b45916.fa | prodigal -d OceanDNA-b45916/cds.fna -a OceanDNA-b45916/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:33:50,395] [INFO] Task succeeded: Prodigal
[2023-03-14 11:33:50,396] [INFO] Task started: HMMsearch
[2023-03-14 11:33:50,396] [INFO] Running command: hmmsearch --tblout OceanDNA-b45916/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference/reference_markers.hmm OceanDNA-b45916/protein.faa > /dev/null
[2023-03-14 11:33:50,584] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:33:50,584] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc415d3f2-da0f-4c94-87fe-d3d1c30df1c9/OceanDNA-b45916.fa]
[2023-03-14 11:33:50,598] [INFO] Query marker FASTA was written to OceanDNA-b45916/markers.fasta
[2023-03-14 11:33:50,598] [INFO] Task started: Blastn
[2023-03-14 11:33:50,598] [INFO] Running command: blastn -query OceanDNA-b45916/markers.fasta -db /var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference/reference_markers.fasta -out OceanDNA-b45916/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:33:51,176] [INFO] Task succeeded: Blastn
[2023-03-14 11:33:51,177] [INFO] Selected 19 target genomes.
[2023-03-14 11:33:51,178] [INFO] Target genome list was writen to OceanDNA-b45916/target_genomes.txt
[2023-03-14 11:33:51,190] [INFO] Task started: fastANI
[2023-03-14 11:33:51,191] [INFO] Running command: fastANI --query /var/lib/cwl/stgc415d3f2-da0f-4c94-87fe-d3d1c30df1c9/OceanDNA-b45916.fa --refList OceanDNA-b45916/target_genomes.txt --output OceanDNA-b45916/fastani_result.tsv --threads 1
[2023-03-14 11:34:03,825] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:03,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:03,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:03,829] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:03,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:03,829] [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
Coraliomargarita sinensis	strain=WN38	GCA_003185655.1	2174842	2174842	type	True	76.7054	75	573	95	below_threshold
Coraliomargarita akajimensis	strain=DSM 45221	GCA_000025905.1	395922	395922	type	True	76.5112	57	573	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:03,829] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45916/tc_result.tsv
[2023-03-14 11:34:03,829] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:03,830] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:03,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference/checkm_data
[2023-03-14 11:34:03,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:03,892] [INFO] Task started: CheckM
[2023-03-14 11:34:03,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45916/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45916/checkm_input OceanDNA-b45916/checkm_result
[2023-03-14 11:34:42,954] [INFO] Task succeeded: CheckM
[2023-03-14 11:34:42,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:34:42,956] [INFO] ===== Completeness check finished =====
[2023-03-14 11:34:42,956] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:34:42,956] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45916/markers.fasta)
[2023-03-14 11:34:42,956] [INFO] Task started: Blastn
[2023-03-14 11:34:42,956] [INFO] Running command: blastn -query OceanDNA-b45916/markers.fasta -db /var/lib/cwl/stgcb38f49e-d973-43a1-978d-f198eb36f2aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45916/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:43,908] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:43,908] [INFO] Selected 8 target genomes.
[2023-03-14 11:34:43,909] [INFO] Target genome list was writen to OceanDNA-b45916/target_genomes_gtdb.txt
[2023-03-14 11:34:43,914] [INFO] Task started: fastANI
[2023-03-14 11:34:43,914] [INFO] Running command: fastANI --query /var/lib/cwl/stgc415d3f2-da0f-4c94-87fe-d3d1c30df1c9/OceanDNA-b45916.fa --refList OceanDNA-b45916/target_genomes_gtdb.txt --output OceanDNA-b45916/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:34:47,531] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:47,537] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:34:47,537] [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_905182465.1	s__UBA7441 sp905182465	86.5923	441	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886465.1	s__UBA7441 sp009886465	85.4798	398	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	97.11	97.11	0.79	0.79	2	-
GCA_003331195.1	s__UBA7441 sp003331195	85.1283	389	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587165.1	s__UBA7441 sp902587165	84.2367	397	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862945.1	s__UBA7441 sp002862945	84.0186	395	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	98.18	98.18	0.82	0.82	2	-
GCA_002729725.1	s__UBA7441 sp002729725	77.9121	174	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__UBA7441	95.0	99.86	99.86	0.96	0.96	2	-
GCA_018607135.1	s__BACL24 sp003485085	77.2264	87	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	99.81	99.81	0.84	0.84	2	-
GCA_905479975.1	s__BACL24 sp905479975	77.0762	91	573	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__DSM-45221;g__BACL24	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:34:47,537] [INFO] GTDB search result was written to OceanDNA-b45916/result_gtdb.tsv
[2023-03-14 11:34:47,537] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:34:47,538] [INFO] DFAST_QC result json was written to OceanDNA-b45916/dqc_result.json
[2023-03-14 11:34:47,538] [INFO] DFAST_QC completed!
[2023-03-14 11:34:47,538] [INFO] Total running time: 0h1m13s