[2023-03-19 01:35:27,746] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:35:27,746] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:35:27,746] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference
[2023-03-19 01:35:29,727] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:35:29,727] [INFO] Task started: Prodigal
[2023-03-19 01:35:29,727] [INFO] Running command: cat /var/lib/cwl/stg364e8194-af17-4192-b372-1d2d4727b375/OceanDNA-b27913.fa | prodigal -d OceanDNA-b27913/cds.fna -a OceanDNA-b27913/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:35:43,659] [INFO] Task succeeded: Prodigal
[2023-03-19 01:35:43,659] [INFO] Task started: HMMsearch
[2023-03-19 01:35:43,659] [INFO] Running command: hmmsearch --tblout OceanDNA-b27913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference/reference_markers.hmm OceanDNA-b27913/protein.faa > /dev/null
[2023-03-19 01:35:43,827] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:35:43,827] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg364e8194-af17-4192-b372-1d2d4727b375/OceanDNA-b27913.fa]
[2023-03-19 01:35:43,843] [INFO] Query marker FASTA was written to OceanDNA-b27913/markers.fasta
[2023-03-19 01:35:43,844] [INFO] Task started: Blastn
[2023-03-19 01:35:43,845] [INFO] Running command: blastn -query OceanDNA-b27913/markers.fasta -db /var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference/reference_markers.fasta -out OceanDNA-b27913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:35:44,420] [INFO] Task succeeded: Blastn
[2023-03-19 01:35:44,420] [INFO] Selected 24 target genomes.
[2023-03-19 01:35:44,421] [INFO] Target genome list was writen to OceanDNA-b27913/target_genomes.txt
[2023-03-19 01:35:44,437] [INFO] Task started: fastANI
[2023-03-19 01:35:44,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg364e8194-af17-4192-b372-1d2d4727b375/OceanDNA-b27913.fa --refList OceanDNA-b27913/target_genomes.txt --output OceanDNA-b27913/fastani_result.tsv --threads 1
[2023-03-19 01:35:58,757] [INFO] Task succeeded: fastANI
[2023-03-19 01:35:58,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:35:58,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:35:58,763] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:35:58,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:35:58,763] [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
Amylibacter ulvae	strain=KCTC 32465	GCA_014652655.1	1651968	1651968	type	True	77.3814	144	727	95	below_threshold
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	77.2564	128	727	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	75.9467	55	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:35:58,763] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27913/tc_result.tsv
[2023-03-19 01:35:58,763] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:35:58,763] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:35:58,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference/checkm_data
[2023-03-19 01:35:58,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:35:59,008] [INFO] Task started: CheckM
[2023-03-19 01:35:59,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27913/checkm_input OceanDNA-b27913/checkm_result
[2023-03-19 01:36:37,619] [INFO] Task succeeded: CheckM
[2023-03-19 01:36:37,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.88%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:36:37,622] [INFO] ===== Completeness check finished =====
[2023-03-19 01:36:37,622] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:36:37,622] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27913/markers.fasta)
[2023-03-19 01:36:37,623] [INFO] Task started: Blastn
[2023-03-19 01:36:37,623] [INFO] Running command: blastn -query OceanDNA-b27913/markers.fasta -db /var/lib/cwl/stgfe759c09-c406-4bc6-ac30-035b5b580936/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:36:38,562] [INFO] Task succeeded: Blastn
[2023-03-19 01:36:38,563] [INFO] Selected 24 target genomes.
[2023-03-19 01:36:38,563] [INFO] Target genome list was writen to OceanDNA-b27913/target_genomes_gtdb.txt
[2023-03-19 01:36:38,587] [INFO] Task started: fastANI
[2023-03-19 01:36:38,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg364e8194-af17-4192-b372-1d2d4727b375/OceanDNA-b27913.fa --refList OceanDNA-b27913/target_genomes_gtdb.txt --output OceanDNA-b27913/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:36:51,396] [INFO] Task succeeded: fastANI
[2023-03-19 01:36:51,402] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:36:51,402] [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_002469545.1	s__Amylibacter sp002469545	99.6003	493	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181935.1	s__Amylibacter sp905181935	77.5382	87	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652655.1	s__Amylibacter ulvae	77.376	142	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742285.1	s__Amylibacter kogurei	77.2227	128	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153745.1	s__Amylibacter sp000153745	76.5236	69	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	98.38	97.19	0.95	0.89	11	-
GCA_018607905.1	s__Amylibacter sp002387535	76.2921	64	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.84	99.84	0.91	0.91	2	-
GCF_011326755.1	s__Halocynthiibacter sp011326755	75.9543	53	727	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:36:51,402] [INFO] GTDB search result was written to OceanDNA-b27913/result_gtdb.tsv
[2023-03-19 01:36:51,402] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:36:51,403] [INFO] DFAST_QC result json was written to OceanDNA-b27913/dqc_result.json
[2023-03-19 01:36:51,404] [INFO] DFAST_QC completed!
[2023-03-19 01:36:51,404] [INFO] Total running time: 0h1m24s