[2023-03-17 14:23:21,327] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:23:21,327] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:23:21,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference
[2023-03-17 14:23:23,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:23:23,907] [INFO] Task started: Prodigal
[2023-03-17 14:23:23,907] [INFO] Running command: cat /var/lib/cwl/stgd6f84936-2514-40e1-9efb-7de8f82a1d99/OceanDNA-b26039.fa | prodigal -d OceanDNA-b26039/cds.fna -a OceanDNA-b26039/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:23:28,634] [INFO] Task succeeded: Prodigal
[2023-03-17 14:23:28,634] [INFO] Task started: HMMsearch
[2023-03-17 14:23:28,634] [INFO] Running command: hmmsearch --tblout OceanDNA-b26039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference/reference_markers.hmm OceanDNA-b26039/protein.faa > /dev/null
[2023-03-17 14:23:28,880] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:23:28,880] [INFO] Found 6/6 markers.
[2023-03-17 14:23:28,892] [INFO] Query marker FASTA was written to OceanDNA-b26039/markers.fasta
[2023-03-17 14:23:28,895] [INFO] Task started: Blastn
[2023-03-17 14:23:28,895] [INFO] Running command: blastn -query OceanDNA-b26039/markers.fasta -db /var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference/reference_markers.fasta -out OceanDNA-b26039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:23:29,622] [INFO] Task succeeded: Blastn
[2023-03-17 14:23:29,622] [INFO] Selected 7 target genomes.
[2023-03-17 14:23:29,623] [INFO] Target genome list was writen to OceanDNA-b26039/target_genomes.txt
[2023-03-17 14:23:29,628] [INFO] Task started: fastANI
[2023-03-17 14:23:29,628] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f84936-2514-40e1-9efb-7de8f82a1d99/OceanDNA-b26039.fa --refList OceanDNA-b26039/target_genomes.txt --output OceanDNA-b26039/fastani_result.tsv --threads 1
[2023-03-17 14:23:32,882] [INFO] Task succeeded: fastANI
[2023-03-17 14:23:32,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 14:23:32,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 14:23:32,883] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 14:23:32,883] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 14:23:32,883] [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 14:23:32,883] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26039/tc_result.tsv
[2023-03-17 14:23:32,883] [INFO] ===== Taxonomy check completed =====
[2023-03-17 14:23:32,883] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:23:32,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference/checkm_data
[2023-03-17 14:23:32,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:23:32,944] [INFO] Task started: CheckM
[2023-03-17 14:23:32,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26039/checkm_input OceanDNA-b26039/checkm_result
[2023-03-17 14:23:59,967] [INFO] Task succeeded: CheckM
[2023-03-17 14:23:59,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.21%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 14:23:59,971] [INFO] ===== Completeness check finished =====
[2023-03-17 14:23:59,971] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:23:59,971] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26039/markers.fasta)
[2023-03-17 14:23:59,973] [INFO] Task started: Blastn
[2023-03-17 14:23:59,973] [INFO] Running command: blastn -query OceanDNA-b26039/markers.fasta -db /var/lib/cwl/stg3a631514-c925-4b52-847c-7c1e346fa6d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:24:01,184] [INFO] Task succeeded: Blastn
[2023-03-17 14:24:01,185] [INFO] Selected 24 target genomes.
[2023-03-17 14:24:01,185] [INFO] Target genome list was writen to OceanDNA-b26039/target_genomes_gtdb.txt
[2023-03-17 14:24:01,299] [INFO] Task started: fastANI
[2023-03-17 14:24:01,299] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6f84936-2514-40e1-9efb-7de8f82a1d99/OceanDNA-b26039.fa --refList OceanDNA-b26039/target_genomes_gtdb.txt --output OceanDNA-b26039/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:24:08,555] [INFO] Task succeeded: fastANI
[2023-03-17 14:24:08,566] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 14:24:08,566] [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	81.9992	146	295	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	80.582	162	295	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	78.575	94	295	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_902583415.1	s__AAA536-G10 sp902583415	78.1445	80	295	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_902592615.1	s__AAA536-G10 sp902592615	77.7744	99	295	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_003284565.1	s__AAA536-G10 sp003284565	77.7276	92	295	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_902530325.1	s__AAA536-G10 sp902530325	77.619	80	295	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	77.5981	75	295	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_902528415.1	s__AAA536-G10 sp902528415	77.4697	92	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.26	95.26	0.64	0.64	2	-
GCA_003278095.1	s__AAA536-G10 sp003278095	77.4356	119	295	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_000384615.1	s__AAA536-G10 sp000384615	77.4216	115	295	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	77.4128	71	295	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	77.4122	61	295	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_003282885.1	s__AAA536-G10 sp003282885	77.3763	85	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.48	96.96	0.85	0.72	3	-
GCA_902622875.1	s__AAA536-G10 sp902622875	77.3146	110	295	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	77.251	122	295	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_003282145.1	s__AAA536-G10 sp003282145	77.2277	114	295	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	77.084	74	295	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_905182395.1	s__CAJJBL01 sp905182395	76.6602	76	295	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__CAJJBL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:24:08,566] [INFO] GTDB search result was written to OceanDNA-b26039/result_gtdb.tsv
[2023-03-17 14:24:08,566] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:24:08,567] [INFO] DFAST_QC result json was written to OceanDNA-b26039/dqc_result.json
[2023-03-17 14:24:08,568] [INFO] DFAST_QC completed!
[2023-03-17 14:24:08,568] [INFO] Total running time: 0h0m47s