[2023-03-16 04:31:43,756] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference
[2023-03-16 04:31:45,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,525] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,525] [INFO] Running command: cat /var/lib/cwl/stg2c41ad11-3c9e-42eb-9ba9-ec6d1ab055c8/OceanDNA-b44043.fa | prodigal -d OceanDNA-b44043/cds.fna -a OceanDNA-b44043/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:31:52,159] [INFO] Task succeeded: Prodigal
[2023-03-16 04:31:52,159] [INFO] Task started: HMMsearch
[2023-03-16 04:31:52,159] [INFO] Running command: hmmsearch --tblout OceanDNA-b44043/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference/reference_markers.hmm OceanDNA-b44043/protein.faa > /dev/null
[2023-03-16 04:31:52,306] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:31:52,307] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2c41ad11-3c9e-42eb-9ba9-ec6d1ab055c8/OceanDNA-b44043.fa]
[2023-03-16 04:31:52,317] [INFO] Query marker FASTA was written to OceanDNA-b44043/markers.fasta
[2023-03-16 04:31:52,318] [INFO] Task started: Blastn
[2023-03-16 04:31:52,318] [INFO] Running command: blastn -query OceanDNA-b44043/markers.fasta -db /var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference/reference_markers.fasta -out OceanDNA-b44043/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:31:52,752] [INFO] Task succeeded: Blastn
[2023-03-16 04:31:52,753] [INFO] Selected 12 target genomes.
[2023-03-16 04:31:52,753] [INFO] Target genome list was writen to OceanDNA-b44043/target_genomes.txt
[2023-03-16 04:31:52,762] [INFO] Task started: fastANI
[2023-03-16 04:31:52,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c41ad11-3c9e-42eb-9ba9-ec6d1ab055c8/OceanDNA-b44043.fa --refList OceanDNA-b44043/target_genomes.txt --output OceanDNA-b44043/fastani_result.tsv --threads 1
[2023-03-16 04:31:59,041] [INFO] Task succeeded: fastANI
[2023-03-16 04:31:59,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:31:59,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:31:59,042] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:31:59,042] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:31:59,042] [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
--------------------------------------------------------------------------------
[2023-03-16 04:31:59,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44043/tc_result.tsv
[2023-03-16 04:31:59,042] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:31:59,042] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:31:59,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference/checkm_data
[2023-03-16 04:31:59,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:31:59,122] [INFO] Task started: CheckM
[2023-03-16 04:31:59,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44043/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44043/checkm_input OceanDNA-b44043/checkm_result
[2023-03-16 04:32:21,920] [INFO] Task succeeded: CheckM
[2023-03-16 04:32:21,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:32:21,926] [INFO] ===== Completeness check finished =====
[2023-03-16 04:32:21,927] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:32:21,927] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44043/markers.fasta)
[2023-03-16 04:32:21,928] [INFO] Task started: Blastn
[2023-03-16 04:32:21,928] [INFO] Running command: blastn -query OceanDNA-b44043/markers.fasta -db /var/lib/cwl/stg2846fab4-701c-46cb-bb44-c5b237c0ce85/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44043/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:22,367] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:22,368] [INFO] Selected 16 target genomes.
[2023-03-16 04:32:22,368] [INFO] Target genome list was writen to OceanDNA-b44043/target_genomes_gtdb.txt
[2023-03-16 04:32:22,387] [INFO] Task started: fastANI
[2023-03-16 04:32:22,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c41ad11-3c9e-42eb-9ba9-ec6d1ab055c8/OceanDNA-b44043.fa --refList OceanDNA-b44043/target_genomes_gtdb.txt --output OceanDNA-b44043/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:32:27,803] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:27,808] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:32:27,808] [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_002718375.1	s__UBA11654 sp002718375	98.9276	205	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	98.63	98.63	0.55	0.55	2	conclusive
GCA_902595845.1	s__UBA11654 sp001629325	93.9669	309	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	96.90	95.86	0.87	0.81	6	-
GCA_902553145.1	s__UBA11654 sp902553145	80.8636	258	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	95.92	95.45	0.83	0.82	5	-
GCA_002691465.1	s__UBA11654 sp002691465	80.8303	260	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	100.00	100.00	0.95	0.95	2	-
GCA_002691305.1	s__UBA11654 sp002691305	79.4071	189	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	97.81	97.81	0.81	0.81	2	-
GCA_002717445.1	s__UBA11654 sp002717445	79.258	200	395	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:32:27,808] [INFO] GTDB search result was written to OceanDNA-b44043/result_gtdb.tsv
[2023-03-16 04:32:27,808] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:32:27,809] [INFO] DFAST_QC result json was written to OceanDNA-b44043/dqc_result.json
[2023-03-16 04:32:27,809] [INFO] DFAST_QC completed!
[2023-03-16 04:32:27,809] [INFO] Total running time: 0h0m44s