[2023-03-15 11:20:29,252] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,253] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference
[2023-03-15 11:20:30,376] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,376] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,377] [INFO] Running command: cat /var/lib/cwl/stgde386bd1-33b9-497a-afed-25f9de5feea6/OceanDNA-b25939.fa | prodigal -d OceanDNA-b25939/cds.fna -a OceanDNA-b25939/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:37,221] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:37,221] [INFO] Task started: HMMsearch
[2023-03-15 11:20:37,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b25939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference/reference_markers.hmm OceanDNA-b25939/protein.faa > /dev/null
[2023-03-15 11:20:37,393] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:37,393] [INFO] Found 6/6 markers.
[2023-03-15 11:20:37,426] [INFO] Query marker FASTA was written to OceanDNA-b25939/markers.fasta
[2023-03-15 11:20:37,428] [INFO] Task started: Blastn
[2023-03-15 11:20:37,428] [INFO] Running command: blastn -query OceanDNA-b25939/markers.fasta -db /var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference/reference_markers.fasta -out OceanDNA-b25939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:37,996] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:37,999] [INFO] Selected 21 target genomes.
[2023-03-15 11:20:38,000] [INFO] Target genome list was writen to OceanDNA-b25939/target_genomes.txt
[2023-03-15 11:20:38,014] [INFO] Task started: fastANI
[2023-03-15 11:20:38,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgde386bd1-33b9-497a-afed-25f9de5feea6/OceanDNA-b25939.fa --refList OceanDNA-b25939/target_genomes.txt --output OceanDNA-b25939/fastani_result.tsv --threads 1
[2023-03-15 11:20:46,043] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:46,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:46,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:46,044] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:46,044] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:20:46,044] [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
--------------------------------------------------------------------------------
[2023-03-15 11:20:46,046] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25939/tc_result.tsv
[2023-03-15 11:20:46,049] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:46,050] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:46,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference/checkm_data
[2023-03-15 11:20:46,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:46,057] [INFO] Task started: CheckM
[2023-03-15 11:20:46,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25939/checkm_input OceanDNA-b25939/checkm_result
[2023-03-15 11:21:09,557] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:09,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:09,611] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:09,612] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:09,612] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25939/markers.fasta)
[2023-03-15 11:21:09,613] [INFO] Task started: Blastn
[2023-03-15 11:21:09,613] [INFO] Running command: blastn -query OceanDNA-b25939/markers.fasta -db /var/lib/cwl/stg100753c9-9e46-477a-9e2d-9b234862b135/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:10,540] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:10,550] [INFO] Selected 22 target genomes.
[2023-03-15 11:21:10,550] [INFO] Target genome list was writen to OceanDNA-b25939/target_genomes_gtdb.txt
[2023-03-15 11:21:10,562] [INFO] Task started: fastANI
[2023-03-15 11:21:10,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgde386bd1-33b9-497a-afed-25f9de5feea6/OceanDNA-b25939.fa --refList OceanDNA-b25939/target_genomes_gtdb.txt --output OceanDNA-b25939/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:16,285] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:16,296] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:21:16,296] [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_905182395.1	s__CAJJBL01 sp905182395	93.2646	269	431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__CAJJBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777705.1	s__AAA536-G10 sp016777705	77.6908	124	431	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	96.71	95.13	0.61	0.57	3	-
GCA_003282145.1	s__AAA536-G10 sp003282145	77.1382	136	431	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_902517275.1	s__AAA536-G10 sp902517275	77.0304	90	431	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	77.0078	135	431	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_902589185.1	s__AAA536-G10 sp902589185	76.9338	95	431	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	76.9148	121	431	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_000421325.1	s__AAA536-G10 sp000421325	76.9121	140	431	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	76.8325	130	431	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_000383115.1	s__AAA536-G10 sp000383115	76.7078	106	431	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_902578805.1	s__AAA536-G10 sp902578805	76.6936	88	431	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_003282435.1	s__AAA536-G10 sp003282435	76.671	91	431	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_902619615.1	s__AAA536-G10 sp902619615	76.6379	142	431	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_902619485.1	s__AAA536-G10 sp902619485	76.5371	103	431	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_902558885.1	s__AAA536-G10 sp902558885	76.5165	124	431	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_902595145.1	s__AAA536-G10 sp902595145	76.5083	107	431	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_902514865.1	s__AAA536-G10 sp902514865	76.5024	73	431	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_902625215.1	s__AAA536-G10 sp902625215	76.4414	119	431	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	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:16,298] [INFO] GTDB search result was written to OceanDNA-b25939/result_gtdb.tsv
[2023-03-15 11:21:16,299] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:16,302] [INFO] DFAST_QC result json was written to OceanDNA-b25939/dqc_result.json
[2023-03-15 11:21:16,302] [INFO] DFAST_QC completed!
[2023-03-15 11:21:16,302] [INFO] Total running time: 0h0m47s