[2023-03-19 04:55:39,414] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference
[2023-03-19 04:55:40,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,561] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,561] [INFO] Running command: cat /var/lib/cwl/stgc8c3260b-7580-49fc-8d0f-60f5a0add5a0/OceanDNA-b42536.fa | prodigal -d OceanDNA-b42536/cds.fna -a OceanDNA-b42536/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:55:47,194] [INFO] Task succeeded: Prodigal
[2023-03-19 04:55:47,194] [INFO] Task started: HMMsearch
[2023-03-19 04:55:47,195] [INFO] Running command: hmmsearch --tblout OceanDNA-b42536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference/reference_markers.hmm OceanDNA-b42536/protein.faa > /dev/null
[2023-03-19 04:55:47,316] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:55:47,317] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc8c3260b-7580-49fc-8d0f-60f5a0add5a0/OceanDNA-b42536.fa]
[2023-03-19 04:55:47,335] [INFO] Query marker FASTA was written to OceanDNA-b42536/markers.fasta
[2023-03-19 04:55:47,336] [INFO] Task started: Blastn
[2023-03-19 04:55:47,336] [INFO] Running command: blastn -query OceanDNA-b42536/markers.fasta -db /var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference/reference_markers.fasta -out OceanDNA-b42536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:55:47,833] [INFO] Task succeeded: Blastn
[2023-03-19 04:55:47,836] [INFO] Selected 6 target genomes.
[2023-03-19 04:55:47,837] [INFO] Target genome list was writen to OceanDNA-b42536/target_genomes.txt
[2023-03-19 04:55:47,843] [INFO] Task started: fastANI
[2023-03-19 04:55:47,843] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8c3260b-7580-49fc-8d0f-60f5a0add5a0/OceanDNA-b42536.fa --refList OceanDNA-b42536/target_genomes.txt --output OceanDNA-b42536/fastani_result.tsv --threads 1
[2023-03-19 04:55:50,924] [INFO] Task succeeded: fastANI
[2023-03-19 04:55:50,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:55:50,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:55:50,925] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:55:50,925] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:55:50,925] [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
--------------------------------------------------------------------------------
[2023-03-19 04:55:50,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42536/tc_result.tsv
[2023-03-19 04:55:50,926] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:55:50,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:55:50,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference/checkm_data
[2023-03-19 04:55:50,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:55:50,934] [INFO] Task started: CheckM
[2023-03-19 04:55:50,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42536/checkm_input OceanDNA-b42536/checkm_result
[2023-03-19 04:56:13,207] [INFO] Task succeeded: CheckM
[2023-03-19 04:56:13,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:56:13,244] [INFO] ===== Completeness check finished =====
[2023-03-19 04:56:13,244] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:56:13,244] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42536/markers.fasta)
[2023-03-19 04:56:13,246] [INFO] Task started: Blastn
[2023-03-19 04:56:13,246] [INFO] Running command: blastn -query OceanDNA-b42536/markers.fasta -db /var/lib/cwl/stg273180b7-e643-4f02-8330-ec3aa79a1299/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:13,873] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:13,878] [INFO] Selected 18 target genomes.
[2023-03-19 04:56:13,878] [INFO] Target genome list was writen to OceanDNA-b42536/target_genomes_gtdb.txt
[2023-03-19 04:56:13,892] [INFO] Task started: fastANI
[2023-03-19 04:56:13,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8c3260b-7580-49fc-8d0f-60f5a0add5a0/OceanDNA-b42536.fa --refList OceanDNA-b42536/target_genomes_gtdb.txt --output OceanDNA-b42536/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:56:18,943] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:18,949] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:56:18,949] [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_003212335.1	s__GCA-2707915 sp003212335	78.4528	147	425	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_902630715.1	s__GCA-2707915 sp902630715	78.4213	131	425	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	77.6276	104	425	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_902574355.1	s__GCA-2707915 sp902574355	77.4602	121	425	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_902618945.1	s__GCA-2707915 sp902618945	77.4046	105	425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.64	95.64	0.79	0.79	2	-
GCA_902605935.1	s__GCA-2707915 sp902605935	77.3456	78	425	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	77.2127	121	425	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_902514295.1	s__GCA-2730855 sp902514295	76.4837	56	425	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:56:18,950] [INFO] GTDB search result was written to OceanDNA-b42536/result_gtdb.tsv
[2023-03-19 04:56:18,950] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:56:18,952] [INFO] DFAST_QC result json was written to OceanDNA-b42536/dqc_result.json
[2023-03-19 04:56:18,952] [INFO] DFAST_QC completed!
[2023-03-19 04:56:18,952] [INFO] Total running time: 0h0m40s