[2023-03-17 03:28:37,108] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:28:37,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:28:37,108] [INFO] DQC Reference Directory: /var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference
[2023-03-17 03:28:38,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:28:38,259] [INFO] Task started: Prodigal
[2023-03-17 03:28:38,259] [INFO] Running command: cat /var/lib/cwl/stgf0a8ca82-6d0b-49b0-a799-b2fe271b02c6/OceanDNA-b23455.fa | prodigal -d OceanDNA-b23455/cds.fna -a OceanDNA-b23455/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:28:49,899] [INFO] Task succeeded: Prodigal
[2023-03-17 03:28:49,899] [INFO] Task started: HMMsearch
[2023-03-17 03:28:49,899] [INFO] Running command: hmmsearch --tblout OceanDNA-b23455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference/reference_markers.hmm OceanDNA-b23455/protein.faa > /dev/null
[2023-03-17 03:28:50,072] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:28:50,073] [INFO] Found 6/6 markers.
[2023-03-17 03:28:50,092] [INFO] Query marker FASTA was written to OceanDNA-b23455/markers.fasta
[2023-03-17 03:28:50,092] [INFO] Task started: Blastn
[2023-03-17 03:28:50,093] [INFO] Running command: blastn -query OceanDNA-b23455/markers.fasta -db /var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference/reference_markers.fasta -out OceanDNA-b23455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:28:50,824] [INFO] Task succeeded: Blastn
[2023-03-17 03:28:50,824] [INFO] Selected 20 target genomes.
[2023-03-17 03:28:50,825] [INFO] Target genome list was writen to OceanDNA-b23455/target_genomes.txt
[2023-03-17 03:28:50,834] [INFO] Task started: fastANI
[2023-03-17 03:28:50,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0a8ca82-6d0b-49b0-a799-b2fe271b02c6/OceanDNA-b23455.fa --refList OceanDNA-b23455/target_genomes.txt --output OceanDNA-b23455/fastani_result.tsv --threads 1
[2023-03-17 03:29:05,234] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:05,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:05,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:05,246] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:05,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:29:05,246] [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
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	80.5543	363	610	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	80.4788	347	610	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	80.2652	371	610	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	80.2516	385	610	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	80.0215	330	610	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	79.7999	364	610	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	79.2328	321	610	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	78.9548	323	610	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	78.9448	328	610	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	78.9326	247	610	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	78.8706	312	610	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	78.8534	322	610	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	78.8276	314	610	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	78.7117	290	610	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	77.7141	208	610	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.684	174	610	95	below_threshold
Brevundimonas subvibrioides	strain=ATCC 15264	GCA_000144605.1	74313	74313	type	True	77.5098	149	610	95	below_threshold
Brevundimonas terrae	strain=DSM 17329	GCA_011761985.1	363631	363631	type	True	76.3779	77	610	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	75.6733	105	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:29:05,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23455/tc_result.tsv
[2023-03-17 03:29:05,247] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:05,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:05,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference/checkm_data
[2023-03-17 03:29:05,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:05,294] [INFO] Task started: CheckM
[2023-03-17 03:29:05,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23455/checkm_input OceanDNA-b23455/checkm_result
[2023-03-17 03:29:36,977] [INFO] Task succeeded: CheckM
[2023-03-17 03:29:36,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:29:36,980] [INFO] ===== Completeness check finished =====
[2023-03-17 03:29:36,980] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:29:36,980] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23455/markers.fasta)
[2023-03-17 03:29:36,981] [INFO] Task started: Blastn
[2023-03-17 03:29:36,982] [INFO] Running command: blastn -query OceanDNA-b23455/markers.fasta -db /var/lib/cwl/stge78e54bd-0926-4db3-bcbe-04c210ecd881/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:38,302] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:38,303] [INFO] Selected 20 target genomes.
[2023-03-17 03:29:38,303] [INFO] Target genome list was writen to OceanDNA-b23455/target_genomes_gtdb.txt
[2023-03-17 03:29:38,324] [INFO] Task started: fastANI
[2023-03-17 03:29:38,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0a8ca82-6d0b-49b0-a799-b2fe271b02c6/OceanDNA-b23455.fa --refList OceanDNA-b23455/target_genomes_gtdb.txt --output OceanDNA-b23455/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:29:52,791] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:52,803] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:29:52,803] [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_013911965.1	s__Phenylobacterium sp013911965	89.1051	541	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_002363865.1	s__Phenylobacterium sp002363865	83.1848	458	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_002441055.1	s__Phenylobacterium sp002441055	81.8527	365	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016772415.1	s__Phenylobacterium sp016772415	80.5358	365	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254505.1	s__Phenylobacterium hankyongense	80.4516	349	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017265.1	s__Phenylobacterium zucineum	80.249	372	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.11	99.11	0.98	0.98	2	-
GCA_018240795.1	s__Phenylobacterium sp018240795	80.1661	332	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425305.1	s__Phenylobacterium sp001425305	80.0683	371	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_003254475.1	s__Phenylobacterium soli	80.0148	330	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	79.9593	325	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822795.1	s__Phenylobacterium sp013822795	79.9565	372	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196295.1	s__Phenylobacterium haematophilum	79.8004	364	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	79.4144	342	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822175.1	s__Phenylobacterium sp903822175	79.3048	303	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.88	99.77	0.95	0.93	4	-
GCF_016467375.1	s__Caulobacter sp016467375	79.1565	243	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	79.0747	310	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	78.6365	286	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424025.1	s__Brevundimonas sp001424025	77.6442	181	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002865.1	s__Brevundimonas sp002002865	77.5082	161	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296955.1	s__Brevundimonas sp004296955	77.2297	187	610	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	95.84	95.71	0.82	0.76	6	-
--------------------------------------------------------------------------------
[2023-03-17 03:29:52,803] [INFO] GTDB search result was written to OceanDNA-b23455/result_gtdb.tsv
[2023-03-17 03:29:52,804] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:29:52,806] [INFO] DFAST_QC result json was written to OceanDNA-b23455/dqc_result.json
[2023-03-17 03:29:52,806] [INFO] DFAST_QC completed!
[2023-03-17 03:29:52,806] [INFO] Total running time: 0h1m16s