[2023-03-14 12:49:51,844] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:49:51,844] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:49:51,844] [INFO] DQC Reference Directory: /var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference
[2023-03-14 12:49:53,130] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:49:53,132] [INFO] Task started: Prodigal
[2023-03-14 12:49:53,132] [INFO] Running command: cat /var/lib/cwl/stg7ffad207-380d-4fc6-bd6e-69976d5e6fa3/OceanDNA-b30047.fa | prodigal -d OceanDNA-b30047/cds.fna -a OceanDNA-b30047/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:50:09,838] [INFO] Task succeeded: Prodigal
[2023-03-14 12:50:09,838] [INFO] Task started: HMMsearch
[2023-03-14 12:50:09,839] [INFO] Running command: hmmsearch --tblout OceanDNA-b30047/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference/reference_markers.hmm OceanDNA-b30047/protein.faa > /dev/null
[2023-03-14 12:50:09,998] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:50:09,998] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ffad207-380d-4fc6-bd6e-69976d5e6fa3/OceanDNA-b30047.fa]
[2023-03-14 12:50:10,019] [INFO] Query marker FASTA was written to OceanDNA-b30047/markers.fasta
[2023-03-14 12:50:10,021] [INFO] Task started: Blastn
[2023-03-14 12:50:10,021] [INFO] Running command: blastn -query OceanDNA-b30047/markers.fasta -db /var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference/reference_markers.fasta -out OceanDNA-b30047/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:50:10,521] [INFO] Task succeeded: Blastn
[2023-03-14 12:50:10,522] [INFO] Selected 24 target genomes.
[2023-03-14 12:50:10,522] [INFO] Target genome list was writen to OceanDNA-b30047/target_genomes.txt
[2023-03-14 12:50:10,535] [INFO] Task started: fastANI
[2023-03-14 12:50:10,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ffad207-380d-4fc6-bd6e-69976d5e6fa3/OceanDNA-b30047.fa --refList OceanDNA-b30047/target_genomes.txt --output OceanDNA-b30047/fastani_result.tsv --threads 1
[2023-03-14 12:50:25,154] [INFO] Task succeeded: fastANI
[2023-03-14 12:50:25,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:50:25,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:50:25,169] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:50:25,169] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:50:25,169] [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
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	78.7035	290	744	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	78.6956	286	744	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	78.6896	266	744	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	78.6745	266	744	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	78.6632	291	744	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	78.6486	266	744	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	78.6051	296	744	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	78.3298	284	744	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.3213	304	744	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	78.2899	286	744	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.0455	267	744	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	77.8048	224	744	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	77.6264	217	744	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.6172	222	744	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	77.5905	219	744	95	below_threshold
Paracoccus aminophilus	strain=JCM 7686	GCA_000444995.1	34003	34003	type	True	77.5285	206	744	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.5116	228	744	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	77.499	230	744	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.3947	207	744	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.3815	208	744	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	77.3244	236	744	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.3157	244	744	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.1488	193	744	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.8765	259	744	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:50:25,169] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30047/tc_result.tsv
[2023-03-14 12:50:25,170] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:50:25,170] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:50:25,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference/checkm_data
[2023-03-14 12:50:25,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:50:25,277] [INFO] Task started: CheckM
[2023-03-14 12:50:25,277] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30047/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30047/checkm_input OceanDNA-b30047/checkm_result
[2023-03-14 12:51:15,415] [INFO] Task succeeded: CheckM
[2023-03-14 12:51:15,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:51:15,420] [INFO] ===== Completeness check finished =====
[2023-03-14 12:51:15,420] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:51:15,420] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30047/markers.fasta)
[2023-03-14 12:51:15,421] [INFO] Task started: Blastn
[2023-03-14 12:51:15,421] [INFO] Running command: blastn -query OceanDNA-b30047/markers.fasta -db /var/lib/cwl/stge7fede4e-c04a-41b2-aa31-93046a1e007e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30047/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:51:16,110] [INFO] Task succeeded: Blastn
[2023-03-14 12:51:16,111] [INFO] Selected 21 target genomes.
[2023-03-14 12:51:16,111] [INFO] Target genome list was writen to OceanDNA-b30047/target_genomes_gtdb.txt
[2023-03-14 12:51:16,198] [INFO] Task started: fastANI
[2023-03-14 12:51:16,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ffad207-380d-4fc6-bd6e-69976d5e6fa3/OceanDNA-b30047.fa --refList OceanDNA-b30047/target_genomes_gtdb.txt --output OceanDNA-b30047/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:51:32,618] [INFO] Task succeeded: fastANI
[2023-03-14 12:51:32,631] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:51:32,631] [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_002422085.1	s__Phaeovulum sp002422085	78.884	274	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001856665.1	s__LPB0142 sp001856665	78.7667	306	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCF_003034995.1	s__Phaeovulum veldkampii	78.6332	267	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_004022265.1	s__Paenirhodobacter ferrireducens	78.5419	287	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	-
GCF_000021865.1	s__Rhodobacter capsulatus_B	78.4854	309	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.13	98.02	0.96	0.92	8	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	78.4588	298	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217355.1	s__Rhodobacter viridis	78.3757	280	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	78.3465	302	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	78.3158	284	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	78.0351	266	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011008935.1	s__KMS-5 sp011008935	77.9894	230	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	77.9675	245	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	77.8032	224	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973825.1	s__Gemmobacter serpentinus	77.6744	225	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100045.1	s__Paracoccus denitrificans	77.6216	216	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_900207575.1	s__Cereibacter_A ovatus	77.6172	222	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000444995.1	s__Paracoccus aminophilus	77.5285	206	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	77.4992	230	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002973535.1	s__Albidovulum denitrificans	77.4467	239	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	77.3057	244	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_012036325.1	s__Tabrizicola sp012036325	76.7546	148	744	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:51:32,632] [INFO] GTDB search result was written to OceanDNA-b30047/result_gtdb.tsv
[2023-03-14 12:51:32,632] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:51:32,635] [INFO] DFAST_QC result json was written to OceanDNA-b30047/dqc_result.json
[2023-03-14 12:51:32,635] [INFO] DFAST_QC completed!
[2023-03-14 12:51:32,635] [INFO] Total running time: 0h1m41s