[2023-03-18 04:24:34,136] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:24:34,142] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:24:34,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference
[2023-03-18 04:24:35,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:24:35,792] [INFO] Task started: Prodigal
[2023-03-18 04:24:35,792] [INFO] Running command: cat /var/lib/cwl/stge5a4db91-2950-4e52-9a9d-2ef65634f68f/OceanDNA-b8476.fa | prodigal -d OceanDNA-b8476/cds.fna -a OceanDNA-b8476/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:24:43,384] [INFO] Task succeeded: Prodigal
[2023-03-18 04:24:43,384] [INFO] Task started: HMMsearch
[2023-03-18 04:24:43,384] [INFO] Running command: hmmsearch --tblout OceanDNA-b8476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference/reference_markers.hmm OceanDNA-b8476/protein.faa > /dev/null
[2023-03-18 04:24:43,552] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:24:43,552] [INFO] Found 6/6 markers.
[2023-03-18 04:24:43,582] [INFO] Query marker FASTA was written to OceanDNA-b8476/markers.fasta
[2023-03-18 04:24:43,582] [INFO] Task started: Blastn
[2023-03-18 04:24:43,582] [INFO] Running command: blastn -query OceanDNA-b8476/markers.fasta -db /var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference/reference_markers.fasta -out OceanDNA-b8476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:24:44,160] [INFO] Task succeeded: Blastn
[2023-03-18 04:24:44,162] [INFO] Selected 31 target genomes.
[2023-03-18 04:24:44,163] [INFO] Target genome list was writen to OceanDNA-b8476/target_genomes.txt
[2023-03-18 04:24:44,179] [INFO] Task started: fastANI
[2023-03-18 04:24:44,179] [INFO] Running command: fastANI --query /var/lib/cwl/stge5a4db91-2950-4e52-9a9d-2ef65634f68f/OceanDNA-b8476.fa --refList OceanDNA-b8476/target_genomes.txt --output OceanDNA-b8476/fastani_result.tsv --threads 1
[2023-03-18 04:24:59,889] [INFO] Task succeeded: fastANI
[2023-03-18 04:24:59,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:24:59,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:24:59,890] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:24:59,890] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:24:59,890] [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
--------------------------------------------------------------------------------
[2023-03-18 04:24:59,892] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8476/tc_result.tsv
[2023-03-18 04:24:59,894] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:24:59,894] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:24:59,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference/checkm_data
[2023-03-18 04:24:59,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:24:59,900] [INFO] Task started: CheckM
[2023-03-18 04:24:59,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8476/checkm_input OceanDNA-b8476/checkm_result
[2023-03-18 04:25:24,225] [INFO] Task succeeded: CheckM
[2023-03-18 04:25:24,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:25:24,318] [INFO] ===== Completeness check finished =====
[2023-03-18 04:25:24,318] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:25:24,318] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8476/markers.fasta)
[2023-03-18 04:25:24,319] [INFO] Task started: Blastn
[2023-03-18 04:25:24,319] [INFO] Running command: blastn -query OceanDNA-b8476/markers.fasta -db /var/lib/cwl/stg9cdc96e4-ecb0-4e9e-a116-dedb8ebdf395/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:25:25,259] [INFO] Task succeeded: Blastn
[2023-03-18 04:25:25,262] [INFO] Selected 10 target genomes.
[2023-03-18 04:25:25,262] [INFO] Target genome list was writen to OceanDNA-b8476/target_genomes_gtdb.txt
[2023-03-18 04:25:25,274] [INFO] Task started: fastANI
[2023-03-18 04:25:25,274] [INFO] Running command: fastANI --query /var/lib/cwl/stge5a4db91-2950-4e52-9a9d-2ef65634f68f/OceanDNA-b8476.fa --refList OceanDNA-b8476/target_genomes_gtdb.txt --output OceanDNA-b8476/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:25:27,622] [INFO] Task succeeded: fastANI
[2023-03-18 04:25:27,628] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:25:27,628] [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_018646865.1	s__MED-G11 sp014239615	99.7615	376	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	conclusive
GCA_902514615.1	s__MED-G11 sp902514615	86.7125	274	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214015.1	s__MED-G11 sp004214015	86.1973	231	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_902509805.1	s__MED-G11 sp902509805	85.6161	188	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_016777325.1	s__MED-G11 sp016777325	85.4371	231	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	84.2166	292	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_002457075.1	s__MED-G11 sp002457075	83.8433	234	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_004213645.1	s__MED-G11 sp004213645	80.5188	228	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.96	97.96	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-18 04:25:27,630] [INFO] GTDB search result was written to OceanDNA-b8476/result_gtdb.tsv
[2023-03-18 04:25:27,632] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:25:27,635] [INFO] DFAST_QC result json was written to OceanDNA-b8476/dqc_result.json
[2023-03-18 04:25:27,635] [INFO] DFAST_QC completed!
[2023-03-18 04:25:27,635] [INFO] Total running time: 0h0m53s