[2023-03-19 00:29:45,968] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:29:45,968] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:29:45,968] [INFO] DQC Reference Directory: /var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference
[2023-03-19 00:29:47,073] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:29:47,073] [INFO] Task started: Prodigal
[2023-03-19 00:29:47,073] [INFO] Running command: cat /var/lib/cwl/stg645f58f4-40da-4ba0-b0c7-db0551bf886e/OceanDNA-b30036.fa | prodigal -d OceanDNA-b30036/cds.fna -a OceanDNA-b30036/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:30:10,117] [INFO] Task succeeded: Prodigal
[2023-03-19 00:30:10,117] [INFO] Task started: HMMsearch
[2023-03-19 00:30:10,117] [INFO] Running command: hmmsearch --tblout OceanDNA-b30036/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference/reference_markers.hmm OceanDNA-b30036/protein.faa > /dev/null
[2023-03-19 00:30:10,315] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:30:10,315] [INFO] Found 6/6 markers.
[2023-03-19 00:30:10,337] [INFO] Query marker FASTA was written to OceanDNA-b30036/markers.fasta
[2023-03-19 00:30:10,338] [INFO] Task started: Blastn
[2023-03-19 00:30:10,338] [INFO] Running command: blastn -query OceanDNA-b30036/markers.fasta -db /var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference/reference_markers.fasta -out OceanDNA-b30036/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:11,024] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:11,025] [INFO] Selected 27 target genomes.
[2023-03-19 00:30:11,025] [INFO] Target genome list was writen to OceanDNA-b30036/target_genomes.txt
[2023-03-19 00:30:11,039] [INFO] Task started: fastANI
[2023-03-19 00:30:11,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg645f58f4-40da-4ba0-b0c7-db0551bf886e/OceanDNA-b30036.fa --refList OceanDNA-b30036/target_genomes.txt --output OceanDNA-b30036/fastani_result.tsv --threads 1
[2023-03-19 00:30:29,100] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:29,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:30:29,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:30:29,115] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:30:29,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:30:29,115] [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
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	78.2627	445	1196	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.1968	441	1196	95	below_threshold
Pseudorhodobacter aquimaris	strain=KCTC 23043	GCA_001202025.1	687412	687412	type	True	78.0722	365	1196	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.0188	368	1196	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	77.9916	401	1196	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	77.9362	404	1196	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	77.9262	415	1196	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.9139	412	1196	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	77.7991	408	1196	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	77.6655	363	1196	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	77.6231	312	1196	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.5766	330	1196	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.5574	333	1196	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	77.5257	326	1196	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4931	329	1196	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	77.4889	349	1196	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.4846	330	1196	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	77.4668	322	1196	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.3755	328	1196	95	below_threshold
Gemmobacter aquaticus	strain=CGMCC 1.7029	GCA_014645295.1	490185	490185	type	True	77.3609	316	1196	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	77.3507	365	1196	95	below_threshold
Pseudorhodobacter antarcticus	strain=KCTC 23700	GCA_001202015.1	1077947	1077947	type	True	77.3037	338	1196	95	below_threshold
Pseudorhodobacter antarcticus	strain=CGMCC 1.10836	GCA_900110135.1	1077947	1077947	type	True	77.2676	344	1196	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	77.2068	289	1196	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	77.1649	266	1196	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	77.1476	294	1196	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7897	290	1196	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:30:29,116] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30036/tc_result.tsv
[2023-03-19 00:30:29,116] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:30:29,116] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:30:29,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference/checkm_data
[2023-03-19 00:30:29,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:30:29,122] [INFO] Task started: CheckM
[2023-03-19 00:30:29,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30036/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30036/checkm_input OceanDNA-b30036/checkm_result
[2023-03-19 00:31:29,197] [INFO] Task succeeded: CheckM
[2023-03-19 00:31:29,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:31:29,200] [INFO] ===== Completeness check finished =====
[2023-03-19 00:31:29,200] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:31:29,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30036/markers.fasta)
[2023-03-19 00:31:29,201] [INFO] Task started: Blastn
[2023-03-19 00:31:29,201] [INFO] Running command: blastn -query OceanDNA-b30036/markers.fasta -db /var/lib/cwl/stg2062fa3a-3663-4eaa-a80a-55cf85e4da2d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30036/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:31:30,294] [INFO] Task succeeded: Blastn
[2023-03-19 00:31:30,295] [INFO] Selected 24 target genomes.
[2023-03-19 00:31:30,295] [INFO] Target genome list was writen to OceanDNA-b30036/target_genomes_gtdb.txt
[2023-03-19 00:31:30,365] [INFO] Task started: fastANI
[2023-03-19 00:31:30,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg645f58f4-40da-4ba0-b0c7-db0551bf886e/OceanDNA-b30036.fa --refList OceanDNA-b30036/target_genomes_gtdb.txt --output OceanDNA-b30036/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:31:46,856] [INFO] Task succeeded: fastANI
[2023-03-19 00:31:46,870] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:31:46,870] [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_003991405.1	s__Pseudorhodobacter sp003991405	78.9453	593	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	78.3517	425	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380135.2	s__Fertoeibacter niger	78.2163	473	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	78.2045	440	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001202025.1	s__Pseudorhodobacter aquimaris	78.0849	363	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	78.0543	387	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001202035.1	s__Pseudorhodobacter wandonensis	77.9917	401	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	77.9281	405	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCA_016792925.1	s__Gemmobacter sp016792925	77.9161	342	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765775.1	s__Pseudorhodobacter sp016765775	77.9026	460	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420745.1	s__Pseudorhodobacter ferrugineus	77.7991	408	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900106675.1	s__Acidimangrovimonas indica	77.6381	307	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004959935.1	s__Falsirhodobacter xinxiangensis	77.6072	268	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.581	331	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	77.4887	349	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060865.1	s__Gemmobacter_B sp003060865	77.4686	321	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841115.1	s__Albidovulum sp002841115	77.4288	354	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005234135.1	s__Pseudorhodobacter turbinis	77.3585	364	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900975.1	s__Tabrizicola aquatica	77.3416	342	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110135.1	s__Pseudorhodobacter antarcticus	77.2781	344	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCA_018057165.1	s__Tabrizicola sp018057165	77.264	241	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407205.1	s__Cereibacter_A sp002407205	77.2318	342	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	77.1134	300	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824055.1	s__Tabrizicola sp013824055	76.7684	228	1196	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	98.98	98.98	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:31:46,870] [INFO] GTDB search result was written to OceanDNA-b30036/result_gtdb.tsv
[2023-03-19 00:31:46,870] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:31:46,873] [INFO] DFAST_QC result json was written to OceanDNA-b30036/dqc_result.json
[2023-03-19 00:31:46,873] [INFO] DFAST_QC completed!
[2023-03-19 00:31:46,873] [INFO] Total running time: 0h2m1s