[2023-03-19 04:43:18,649] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,649] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,649] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference
[2023-03-19 04:43:19,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,841] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,841] [INFO] Running command: cat /var/lib/cwl/stg660c5843-3280-4d00-91a6-9ed5a99f4a5b/OceanDNA-b30091.fa | prodigal -d OceanDNA-b30091/cds.fna -a OceanDNA-b30091/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:30,502] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:30,502] [INFO] Task started: HMMsearch
[2023-03-19 04:43:30,502] [INFO] Running command: hmmsearch --tblout OceanDNA-b30091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference/reference_markers.hmm OceanDNA-b30091/protein.faa > /dev/null
[2023-03-19 04:43:30,673] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:30,673] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg660c5843-3280-4d00-91a6-9ed5a99f4a5b/OceanDNA-b30091.fa]
[2023-03-19 04:43:30,693] [INFO] Query marker FASTA was written to OceanDNA-b30091/markers.fasta
[2023-03-19 04:43:30,694] [INFO] Task started: Blastn
[2023-03-19 04:43:30,695] [INFO] Running command: blastn -query OceanDNA-b30091/markers.fasta -db /var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference/reference_markers.fasta -out OceanDNA-b30091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:31,265] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:31,266] [INFO] Selected 20 target genomes.
[2023-03-19 04:43:31,266] [INFO] Target genome list was writen to OceanDNA-b30091/target_genomes.txt
[2023-03-19 04:43:31,278] [INFO] Task started: fastANI
[2023-03-19 04:43:31,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg660c5843-3280-4d00-91a6-9ed5a99f4a5b/OceanDNA-b30091.fa --refList OceanDNA-b30091/target_genomes.txt --output OceanDNA-b30091/fastani_result.tsv --threads 1
[2023-03-19 04:43:43,832] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:43,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:43,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:43,842] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:43,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:43,842] [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 faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.2086	114	471	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.1318	86	471	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	76.973	126	471	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.9415	127	471	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	76.9376	127	471	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.916	68	471	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.7767	101	471	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.7464	91	471	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	76.7244	84	471	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.6651	121	471	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.6439	111	471	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.6246	112	471	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	76.568	110	471	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.5634	89	471	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.4138	75	471	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:43,842] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30091/tc_result.tsv
[2023-03-19 04:43:43,843] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:43,843] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:43,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference/checkm_data
[2023-03-19 04:43:43,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:43,955] [INFO] Task started: CheckM
[2023-03-19 04:43:43,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30091/checkm_input OceanDNA-b30091/checkm_result
[2023-03-19 04:44:15,452] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:15,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.32%
Contamintation: 2.98%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-19 04:44:15,454] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:15,455] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:15,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30091/markers.fasta)
[2023-03-19 04:44:15,456] [INFO] Task started: Blastn
[2023-03-19 04:44:15,456] [INFO] Running command: blastn -query OceanDNA-b30091/markers.fasta -db /var/lib/cwl/stgbcc800d2-029b-4817-b257-e977598252f1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:16,306] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:16,307] [INFO] Selected 22 target genomes.
[2023-03-19 04:44:16,307] [INFO] Target genome list was writen to OceanDNA-b30091/target_genomes_gtdb.txt
[2023-03-19 04:44:16,388] [INFO] Task started: fastANI
[2023-03-19 04:44:16,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg660c5843-3280-4d00-91a6-9ed5a99f4a5b/OceanDNA-b30091.fa --refList OceanDNA-b30091/target_genomes_gtdb.txt --output OceanDNA-b30091/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:30,083] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:30,094] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:44:30,094] [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
GCF_009762325.1	s__Roseovarius faecimaris	77.2588	112	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	77.1318	86	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.029	85	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363715.1	s__Roseovarius sp009363715	76.9508	102	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	76.9415	127	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.916	68	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	76.8608	77	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900172365.1	s__Roseovarius gaetbuli	76.8533	75	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172285.1	s__Roseovarius aestuarii	76.7019	91	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	76.6741	115	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_005434965.1	s__Marimonas lutisalis	76.67	89	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	76.6651	121	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_900172255.1	s__Roseovarius halotolerans	76.6246	112	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005938215.1	s__Ruegeria sediminis	76.6155	76	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.5854	55	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441615.1	s__Roseovarius atlanticus	76.568	110	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.5634	89	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	76.517	78	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142625.1	s__Roseovarius marisflavi	76.4084	73	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	76.2987	50	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:30,095] [INFO] GTDB search result was written to OceanDNA-b30091/result_gtdb.tsv
[2023-03-19 04:44:30,095] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:30,097] [INFO] DFAST_QC result json was written to OceanDNA-b30091/dqc_result.json
[2023-03-19 04:44:30,097] [INFO] DFAST_QC completed!
[2023-03-19 04:44:30,097] [INFO] Total running time: 0h1m11s