[2023-03-18 08:17:18,479] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,479] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference
[2023-03-18 08:17:20,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,265] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,265] [INFO] Running command: cat /var/lib/cwl/stg7fe78a03-5f86-44c0-9b76-18842fc843ed/OceanDNA-b28981.fa | prodigal -d OceanDNA-b28981/cds.fna -a OceanDNA-b28981/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:38,176] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:38,176] [INFO] Task started: HMMsearch
[2023-03-18 08:17:38,176] [INFO] Running command: hmmsearch --tblout OceanDNA-b28981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference/reference_markers.hmm OceanDNA-b28981/protein.faa > /dev/null
[2023-03-18 08:17:38,373] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:38,374] [INFO] Found 6/6 markers.
[2023-03-18 08:17:38,392] [INFO] Query marker FASTA was written to OceanDNA-b28981/markers.fasta
[2023-03-18 08:17:38,392] [INFO] Task started: Blastn
[2023-03-18 08:17:38,393] [INFO] Running command: blastn -query OceanDNA-b28981/markers.fasta -db /var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference/reference_markers.fasta -out OceanDNA-b28981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:38,958] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:38,959] [INFO] Selected 34 target genomes.
[2023-03-18 08:17:38,959] [INFO] Target genome list was writen to OceanDNA-b28981/target_genomes.txt
[2023-03-18 08:17:38,973] [INFO] Task started: fastANI
[2023-03-18 08:17:38,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fe78a03-5f86-44c0-9b76-18842fc843ed/OceanDNA-b28981.fa --refList OceanDNA-b28981/target_genomes.txt --output OceanDNA-b28981/fastani_result.tsv --threads 1
[2023-03-18 08:17:57,944] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:57,944] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:57,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:57,950] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:57,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:57,950] [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
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.1253	56	967	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.1117	66	967	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	75.8397	70	967	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	75.7958	51	967	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	75.7658	60	967	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	75.6337	61	967	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	75.5559	50	967	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:57,950] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28981/tc_result.tsv
[2023-03-18 08:17:57,950] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:57,951] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:57,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference/checkm_data
[2023-03-18 08:17:57,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:57,956] [INFO] Task started: CheckM
[2023-03-18 08:17:57,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28981/checkm_input OceanDNA-b28981/checkm_result
[2023-03-18 08:18:44,444] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:44,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:44,446] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:44,446] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:44,447] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28981/markers.fasta)
[2023-03-18 08:18:44,447] [INFO] Task started: Blastn
[2023-03-18 08:18:44,447] [INFO] Running command: blastn -query OceanDNA-b28981/markers.fasta -db /var/lib/cwl/stg7ac5a0a3-8311-49d1-84b3-535c13b694bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:45,233] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:45,234] [INFO] Selected 22 target genomes.
[2023-03-18 08:18:45,234] [INFO] Target genome list was writen to OceanDNA-b28981/target_genomes_gtdb.txt
[2023-03-18 08:18:45,271] [INFO] Task started: fastANI
[2023-03-18 08:18:45,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fe78a03-5f86-44c0-9b76-18842fc843ed/OceanDNA-b28981.fa --refList OceanDNA-b28981/target_genomes_gtdb.txt --output OceanDNA-b28981/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:18:58,854] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:58,862] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:18:58,862] [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_001642945.1	s__LGRT01 sp001642945	98.9837	920	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	conclusive
GCA_016778765.1	s__LGRT01 sp016778765	93.4301	769	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	98.26	96.00	0.81	0.61	8	-
GCA_002726375.1	s__CABZJG01 sp002726375	76.6891	73	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	-
GCA_902525995.1	s__CABZJG01 sp902525995	76.6418	53	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000472185.1	s__HIMB11 sp000472185	76.2761	62	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.1946	50	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684375.1	s__CPC320 sp002684375	76.1251	69	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.52	98.26	0.79	0.72	8	-
GCF_900172365.1	s__Roseovarius gaetbuli	76.1117	66	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.0403	65	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	75.916	60	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	75.8196	71	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	75.7958	51	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	75.6337	61	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	75.5559	50	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:18:58,862] [INFO] GTDB search result was written to OceanDNA-b28981/result_gtdb.tsv
[2023-03-18 08:18:58,862] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:18:58,864] [INFO] DFAST_QC result json was written to OceanDNA-b28981/dqc_result.json
[2023-03-18 08:18:58,864] [INFO] DFAST_QC completed!
[2023-03-18 08:18:58,864] [INFO] Total running time: 0h1m40s