[2023-03-17 00:45:47,256] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,257] [INFO] DQC Reference Directory: /var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference
[2023-03-17 00:45:48,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,376] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,376] [INFO] Running command: cat /var/lib/cwl/stgb896b6ab-653c-4037-8738-3db82af8543f/OceanDNA-b32497.fa | prodigal -d OceanDNA-b32497/cds.fna -a OceanDNA-b32497/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:53,448] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:53,448] [INFO] Task started: HMMsearch
[2023-03-17 00:45:53,448] [INFO] Running command: hmmsearch --tblout OceanDNA-b32497/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference/reference_markers.hmm OceanDNA-b32497/protein.faa > /dev/null
[2023-03-17 00:45:53,646] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:53,647] [INFO] Found 6/6 markers.
[2023-03-17 00:45:53,656] [INFO] Query marker FASTA was written to OceanDNA-b32497/markers.fasta
[2023-03-17 00:45:53,658] [INFO] Task started: Blastn
[2023-03-17 00:45:53,658] [INFO] Running command: blastn -query OceanDNA-b32497/markers.fasta -db /var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference/reference_markers.fasta -out OceanDNA-b32497/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:54,485] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:54,486] [INFO] Selected 18 target genomes.
[2023-03-17 00:45:54,486] [INFO] Target genome list was writen to OceanDNA-b32497/target_genomes.txt
[2023-03-17 00:45:54,624] [INFO] Task started: fastANI
[2023-03-17 00:45:54,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgb896b6ab-653c-4037-8738-3db82af8543f/OceanDNA-b32497.fa --refList OceanDNA-b32497/target_genomes.txt --output OceanDNA-b32497/fastani_result.tsv --threads 1
[2023-03-17 00:46:03,119] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:03,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:03,120] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:03,120] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:03,120] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:03,120] [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
--------------------------------------------------------------------------------
[2023-03-17 00:46:03,120] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32497/tc_result.tsv
[2023-03-17 00:46:03,120] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:03,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:03,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference/checkm_data
[2023-03-17 00:46:03,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:03,126] [INFO] Task started: CheckM
[2023-03-17 00:46:03,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32497/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32497/checkm_input OceanDNA-b32497/checkm_result
[2023-03-17 00:46:24,888] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:24,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:24,890] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:24,890] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:24,890] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32497/markers.fasta)
[2023-03-17 00:46:24,892] [INFO] Task started: Blastn
[2023-03-17 00:46:24,892] [INFO] Running command: blastn -query OceanDNA-b32497/markers.fasta -db /var/lib/cwl/stge04605fc-a2e7-4579-996c-9db8db1be5f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32497/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:26,433] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:26,434] [INFO] Selected 27 target genomes.
[2023-03-17 00:46:26,434] [INFO] Target genome list was writen to OceanDNA-b32497/target_genomes_gtdb.txt
[2023-03-17 00:46:27,084] [INFO] Task started: fastANI
[2023-03-17 00:46:27,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgb896b6ab-653c-4037-8738-3db82af8543f/OceanDNA-b32497.fa --refList OceanDNA-b32497/target_genomes_gtdb.txt --output OceanDNA-b32497/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:33,094] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:33,099] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:46:33,099] [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_002689325.1	s__GCA-002690875 sp002689325	77.0532	143	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902536485.1	s__GCA-002690875 sp902536485	77.0088	98	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690875.1	s__GCA-002690875 sp002690875	76.9595	117	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563505.1	s__GCA-2711515 sp902563505	76.5279	80	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2711515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712255.1	s__MED-G10 sp002712255	76.1393	78	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536655.1	s__GCA-2691245 sp902536655	75.9774	57	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563305.1	s__GCA-2691245 sp902563305	75.8839	55	337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:33,099] [INFO] GTDB search result was written to OceanDNA-b32497/result_gtdb.tsv
[2023-03-17 00:46:33,099] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:33,100] [INFO] DFAST_QC result json was written to OceanDNA-b32497/dqc_result.json
[2023-03-17 00:46:33,100] [INFO] DFAST_QC completed!
[2023-03-17 00:46:33,100] [INFO] Total running time: 0h0m46s