[2023-03-19 00:19:08,848] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,848] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,848] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference
[2023-03-19 00:19:10,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,374] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,374] [INFO] Running command: cat /var/lib/cwl/stg24601a6a-3dfb-454e-bd16-82a76cbf84ed/OceanDNA-b28107.fa | prodigal -d OceanDNA-b28107/cds.fna -a OceanDNA-b28107/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:22,406] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:22,407] [INFO] Task started: HMMsearch
[2023-03-19 00:19:22,407] [INFO] Running command: hmmsearch --tblout OceanDNA-b28107/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference/reference_markers.hmm OceanDNA-b28107/protein.faa > /dev/null
[2023-03-19 00:19:22,577] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:22,578] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg24601a6a-3dfb-454e-bd16-82a76cbf84ed/OceanDNA-b28107.fa]
[2023-03-19 00:19:22,598] [INFO] Query marker FASTA was written to OceanDNA-b28107/markers.fasta
[2023-03-19 00:19:22,598] [INFO] Task started: Blastn
[2023-03-19 00:19:22,599] [INFO] Running command: blastn -query OceanDNA-b28107/markers.fasta -db /var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference/reference_markers.fasta -out OceanDNA-b28107/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:23,191] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:23,192] [INFO] Selected 22 target genomes.
[2023-03-19 00:19:23,192] [INFO] Target genome list was writen to OceanDNA-b28107/target_genomes.txt
[2023-03-19 00:19:23,207] [INFO] Task started: fastANI
[2023-03-19 00:19:23,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg24601a6a-3dfb-454e-bd16-82a76cbf84ed/OceanDNA-b28107.fa --refList OceanDNA-b28107/target_genomes.txt --output OceanDNA-b28107/fastani_result.tsv --threads 1
[2023-03-19 00:19:36,993] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:36,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:36,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:37,001] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 00:19:37,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 00:19:37,001] [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
Celeribacter baekdonensis	strain=DSM 27375	GCA_900102315.1	875171	875171	type	True	99.8752	396	409	95	conclusive
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	79.0901	203	409	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	78.9992	196	409	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	78.9516	187	409	95	below_threshold
Celeribacter halophilus	strain=CGMCC 1.8891	GCA_900114135.1	576117	576117	type	True	78.8064	163	409	95	below_threshold
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	78.7748	166	409	95	below_threshold
Thioclava indica	strain=DT23-4	GCA_000714545.1	1353528	1353528	type	True	76.9397	62	409	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	76.9016	52	409	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.6609	57	409	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.494	51	409	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:19:37,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28107/tc_result.tsv
[2023-03-19 00:19:37,002] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:37,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:37,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference/checkm_data
[2023-03-19 00:19:37,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:37,007] [INFO] Task started: CheckM
[2023-03-19 00:19:37,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28107/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28107/checkm_input OceanDNA-b28107/checkm_result
[2023-03-19 00:20:11,736] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:11,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:11,740] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:11,740] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:11,740] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28107/markers.fasta)
[2023-03-19 00:20:11,741] [INFO] Task started: Blastn
[2023-03-19 00:20:11,741] [INFO] Running command: blastn -query OceanDNA-b28107/markers.fasta -db /var/lib/cwl/stg7f392b71-d46d-4beb-b98a-96ab13e34941/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28107/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:12,681] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:12,681] [INFO] Selected 9 target genomes.
[2023-03-19 00:20:12,681] [INFO] Target genome list was writen to OceanDNA-b28107/target_genomes_gtdb.txt
[2023-03-19 00:20:12,688] [INFO] Task started: fastANI
[2023-03-19 00:20:12,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg24601a6a-3dfb-454e-bd16-82a76cbf84ed/OceanDNA-b28107.fa --refList OceanDNA-b28107/target_genomes_gtdb.txt --output OceanDNA-b28107/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:20:18,698] [INFO] Task succeeded: fastANI
[2023-03-19 00:20:18,702] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:20:18,703] [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_900102315.1	s__Celeribacter baekdonensis	99.8752	396	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.81	97.75	0.91	0.89	8	conclusive
GCF_000299875.1	s__Celeribacter baekdonensis_A	93.8188	358	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	99.07	99.01	0.95	0.93	3	-
GCF_003047105.1	s__Celeribacter baekdonensis_B	89.7344	329	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806455.1	s__Celeribacter sp011806455	79.5001	215	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_900113955.1	s__Celeribacter neptunius	79.0901	203	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550095.1	s__Celeribacter ethanolicus	78.9992	196	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900114135.1	s__Celeribacter halophilus	78.8064	163	409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	-
--------------------------------------------------------------------------------
[2023-03-19 00:20:18,998] [INFO] GTDB search result was written to OceanDNA-b28107/result_gtdb.tsv
[2023-03-19 00:20:18,998] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:20:18,999] [INFO] DFAST_QC result json was written to OceanDNA-b28107/dqc_result.json
[2023-03-19 00:20:19,000] [INFO] DFAST_QC completed!
[2023-03-19 00:20:19,000] [INFO] Total running time: 0h1m10s