[2023-03-19 04:43:18,639] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,640] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,640] [INFO] DQC Reference Directory: /var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference
[2023-03-19 04:43:19,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,785] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,786] [INFO] Running command: cat /var/lib/cwl/stg756fd4f7-eaed-409d-9c90-2072d4a3e6ee/OceanDNA-b26049.fa | prodigal -d OceanDNA-b26049/cds.fna -a OceanDNA-b26049/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:22,966] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:22,966] [INFO] Task started: HMMsearch
[2023-03-19 04:43:22,966] [INFO] Running command: hmmsearch --tblout OceanDNA-b26049/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference/reference_markers.hmm OceanDNA-b26049/protein.faa > /dev/null
[2023-03-19 04:43:23,130] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:23,130] [INFO] Found 6/6 markers.
[2023-03-19 04:43:23,140] [INFO] Query marker FASTA was written to OceanDNA-b26049/markers.fasta
[2023-03-19 04:43:23,141] [INFO] Task started: Blastn
[2023-03-19 04:43:23,141] [INFO] Running command: blastn -query OceanDNA-b26049/markers.fasta -db /var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference/reference_markers.fasta -out OceanDNA-b26049/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:23,760] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:23,761] [INFO] Selected 13 target genomes.
[2023-03-19 04:43:23,761] [INFO] Target genome list was writen to OceanDNA-b26049/target_genomes.txt
[2023-03-19 04:43:23,768] [INFO] Task started: fastANI
[2023-03-19 04:43:23,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg756fd4f7-eaed-409d-9c90-2072d4a3e6ee/OceanDNA-b26049.fa --refList OceanDNA-b26049/target_genomes.txt --output OceanDNA-b26049/fastani_result.tsv --threads 1
[2023-03-19 04:43:29,312] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:29,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:29,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:29,313] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:29,313] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:43:29,313] [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 04:43:29,313] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26049/tc_result.tsv
[2023-03-19 04:43:29,313] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:29,313] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:29,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference/checkm_data
[2023-03-19 04:43:29,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:29,336] [INFO] Task started: CheckM
[2023-03-19 04:43:29,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26049/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26049/checkm_input OceanDNA-b26049/checkm_result
[2023-03-19 04:43:45,900] [INFO] Task succeeded: CheckM
[2023-03-19 04:43:45,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 5.85%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-03-19 04:43:45,902] [INFO] ===== Completeness check finished =====
[2023-03-19 04:43:45,902] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:43:45,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26049/markers.fasta)
[2023-03-19 04:43:45,903] [INFO] Task started: Blastn
[2023-03-19 04:43:45,903] [INFO] Running command: blastn -query OceanDNA-b26049/markers.fasta -db /var/lib/cwl/stga20cb18c-205c-4e63-b3f7-3a776d513243/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26049/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:46,834] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:46,835] [INFO] Selected 23 target genomes.
[2023-03-19 04:43:46,835] [INFO] Target genome list was writen to OceanDNA-b26049/target_genomes_gtdb.txt
[2023-03-19 04:43:46,913] [INFO] Task started: fastANI
[2023-03-19 04:43:46,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg756fd4f7-eaed-409d-9c90-2072d4a3e6ee/OceanDNA-b26049.fa --refList OceanDNA-b26049/target_genomes_gtdb.txt --output OceanDNA-b26049/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:43:52,310] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:52,318] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:43:52,318] [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_002691185.1	s__AAA536-G10 sp002691185	91.5445	85	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777645.1	s__AAA536-G10 sp016777645	79.7453	79	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619805.1	s__AAA536-G10 sp902619805	77.4139	58	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	77.3574	54	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902619615.1	s__AAA536-G10 sp902619615	77.3006	66	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	77.2354	54	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278095.1	s__AAA536-G10 sp003278095	77.1614	64	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_003282145.1	s__AAA536-G10 sp003282145	77.0309	53	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902592615.1	s__AAA536-G10 sp902592615	76.9832	50	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622875.1	s__AAA536-G10 sp902622875	76.8739	51	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616615.1	s__AAA536-G10 sp902616615	76.8058	54	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517815.1	s__AAA536-G10 sp902517815	76.6674	54	137	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:43:52,318] [INFO] GTDB search result was written to OceanDNA-b26049/result_gtdb.tsv
[2023-03-19 04:43:52,318] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:43:52,319] [INFO] DFAST_QC result json was written to OceanDNA-b26049/dqc_result.json
[2023-03-19 04:43:52,320] [INFO] DFAST_QC completed!
[2023-03-19 04:43:52,320] [INFO] Total running time: 0h0m34s