[2023-03-15 03:56:21,767] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,767] [INFO] DQC Reference Directory: /var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference
[2023-03-15 03:56:23,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,406] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,406] [INFO] Running command: cat /var/lib/cwl/stg84decc2a-7e29-4b90-8db2-fe4628ccca3f/OceanDNA-b42531.fa | prodigal -d OceanDNA-b42531/cds.fna -a OceanDNA-b42531/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:27,484] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:27,484] [INFO] Task started: HMMsearch
[2023-03-15 03:56:27,484] [INFO] Running command: hmmsearch --tblout OceanDNA-b42531/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference/reference_markers.hmm OceanDNA-b42531/protein.faa > /dev/null
[2023-03-15 03:56:27,666] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:27,666] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg84decc2a-7e29-4b90-8db2-fe4628ccca3f/OceanDNA-b42531.fa]
[2023-03-15 03:56:27,675] [INFO] Query marker FASTA was written to OceanDNA-b42531/markers.fasta
[2023-03-15 03:56:27,675] [INFO] Task started: Blastn
[2023-03-15 03:56:27,675] [INFO] Running command: blastn -query OceanDNA-b42531/markers.fasta -db /var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference/reference_markers.fasta -out OceanDNA-b42531/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:29,089] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:29,089] [INFO] Selected 15 target genomes.
[2023-03-15 03:56:29,090] [INFO] Target genome list was writen to OceanDNA-b42531/target_genomes.txt
[2023-03-15 03:56:29,106] [INFO] Task started: fastANI
[2023-03-15 03:56:29,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg84decc2a-7e29-4b90-8db2-fe4628ccca3f/OceanDNA-b42531.fa --refList OceanDNA-b42531/target_genomes.txt --output OceanDNA-b42531/fastani_result.tsv --threads 1
[2023-03-15 03:56:33,878] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:33,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:33,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:33,879] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:33,879] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:56:33,879] [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
--------------------------------------------------------------------------------
[2023-03-15 03:56:33,879] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42531/tc_result.tsv
[2023-03-15 03:56:33,879] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:33,879] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:33,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference/checkm_data
[2023-03-15 03:56:33,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:33,884] [INFO] Task started: CheckM
[2023-03-15 03:56:33,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42531/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42531/checkm_input OceanDNA-b42531/checkm_result
[2023-03-15 03:56:50,335] [INFO] Task succeeded: CheckM
[2023-03-15 03:56:50,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:56:50,337] [INFO] ===== Completeness check finished =====
[2023-03-15 03:56:50,337] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:56:50,337] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42531/markers.fasta)
[2023-03-15 03:56:50,337] [INFO] Task started: Blastn
[2023-03-15 03:56:50,337] [INFO] Running command: blastn -query OceanDNA-b42531/markers.fasta -db /var/lib/cwl/stge4c5344d-14ce-4286-ad44-6b357a58919f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42531/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:51,068] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:51,069] [INFO] Selected 21 target genomes.
[2023-03-15 03:56:51,069] [INFO] Target genome list was writen to OceanDNA-b42531/target_genomes_gtdb.txt
[2023-03-15 03:56:51,119] [INFO] Task started: fastANI
[2023-03-15 03:56:51,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg84decc2a-7e29-4b90-8db2-fe4628ccca3f/OceanDNA-b42531.fa --refList OceanDNA-b42531/target_genomes_gtdb.txt --output OceanDNA-b42531/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:56:56,645] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:56,652] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:56:56,652] [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_902517565.1	s__GCA-2707915 sp902517565	79.2005	98	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777005.1	s__GCA-2707915 sp016777005	78.7223	71	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212335.1	s__GCA-2707915 sp003212335	78.0136	94	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
GCA_902605935.1	s__GCA-2707915 sp902605935	77.7584	61	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542325.1	s__GCA-2707915 sp902542325	77.6326	102	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902574355.1	s__GCA-2707915 sp902574355	77.6246	106	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606175.1	s__GCA-2707915 sp902606175	77.3977	103	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.3006	100	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902620785.1	s__GCA-2707915 sp902620785	77.0745	99	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
GCA_902630715.1	s__GCA-2707915 sp902630715	76.9825	53	264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:56:56,652] [INFO] GTDB search result was written to OceanDNA-b42531/result_gtdb.tsv
[2023-03-15 03:56:56,653] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:56:56,653] [INFO] DFAST_QC result json was written to OceanDNA-b42531/dqc_result.json
[2023-03-15 03:56:56,654] [INFO] DFAST_QC completed!
[2023-03-15 03:56:56,654] [INFO] Total running time: 0h0m35s