[2023-03-16 01:21:12,498] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:21:12,498] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:21:12,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference
[2023-03-16 01:21:13,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:21:13,664] [INFO] Task started: Prodigal
[2023-03-16 01:21:13,665] [INFO] Running command: cat /var/lib/cwl/stg1b646854-1511-4747-9846-8656a281c599/OceanDNA-b513.fa | prodigal -d OceanDNA-b513/cds.fna -a OceanDNA-b513/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:21:37,620] [INFO] Task succeeded: Prodigal
[2023-03-16 01:21:37,620] [INFO] Task started: HMMsearch
[2023-03-16 01:21:37,620] [INFO] Running command: hmmsearch --tblout OceanDNA-b513/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference/reference_markers.hmm OceanDNA-b513/protein.faa > /dev/null
[2023-03-16 01:21:37,813] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:21:37,813] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1b646854-1511-4747-9846-8656a281c599/OceanDNA-b513.fa]
[2023-03-16 01:21:37,845] [INFO] Query marker FASTA was written to OceanDNA-b513/markers.fasta
[2023-03-16 01:21:37,845] [INFO] Task started: Blastn
[2023-03-16 01:21:37,845] [INFO] Running command: blastn -query OceanDNA-b513/markers.fasta -db /var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference/reference_markers.fasta -out OceanDNA-b513/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:21:38,458] [INFO] Task succeeded: Blastn
[2023-03-16 01:21:38,460] [INFO] Selected 16 target genomes.
[2023-03-16 01:21:38,460] [INFO] Target genome list was writen to OceanDNA-b513/target_genomes.txt
[2023-03-16 01:21:38,478] [INFO] Task started: fastANI
[2023-03-16 01:21:38,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b646854-1511-4747-9846-8656a281c599/OceanDNA-b513.fa --refList OceanDNA-b513/target_genomes.txt --output OceanDNA-b513/fastani_result.tsv --threads 1
[2023-03-16 01:21:52,908] [INFO] Task succeeded: fastANI
[2023-03-16 01:21:52,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:21:52,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:21:52,917] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:21:52,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 01:21:52,917] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.9463	418	1230	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.0031	252	1230	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.8333	205	1230	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.6157	245	1230	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.9748	116	1230	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.9446	115	1230	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	75.1589	65	1230	95	below_threshold
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	75.1183	77	1230	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	75.1169	66	1230	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	75.0977	68	1230	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	75.0881	69	1230	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	75.0313	72	1230	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	74.8573	65	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:21:52,918] [INFO] DFAST Taxonomy check result was written to OceanDNA-b513/tc_result.tsv
[2023-03-16 01:21:52,927] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:21:52,927] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:21:52,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference/checkm_data
[2023-03-16 01:21:52,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:21:52,940] [INFO] Task started: CheckM
[2023-03-16 01:21:52,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b513/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b513/checkm_input OceanDNA-b513/checkm_result
[2023-03-16 01:22:54,438] [INFO] Task succeeded: CheckM
[2023-03-16 01:22:54,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:22:54,570] [INFO] ===== Completeness check finished =====
[2023-03-16 01:22:54,571] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:22:54,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b513/markers.fasta)
[2023-03-16 01:22:54,572] [INFO] Task started: Blastn
[2023-03-16 01:22:54,572] [INFO] Running command: blastn -query OceanDNA-b513/markers.fasta -db /var/lib/cwl/stgb899f5d1-d378-460f-87b8-b787d2ca6f52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b513/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:22:55,469] [INFO] Task succeeded: Blastn
[2023-03-16 01:22:55,472] [INFO] Selected 15 target genomes.
[2023-03-16 01:22:55,472] [INFO] Target genome list was writen to OceanDNA-b513/target_genomes_gtdb.txt
[2023-03-16 01:22:55,668] [INFO] Task started: fastANI
[2023-03-16 01:22:55,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b646854-1511-4747-9846-8656a281c599/OceanDNA-b513.fa --refList OceanDNA-b513/target_genomes_gtdb.txt --output OceanDNA-b513/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:23:04,576] [INFO] Task succeeded: fastANI
[2023-03-16 01:23:04,585] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:23:04,585] [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_004364865.1	s__Ilumatobacter fluminis	77.9492	419	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	77.7134	338	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.3869	235	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.326	229	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	77.0923	237	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.0138	251	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	76.8342	205	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013811855.1	s__JACCUL01 sp013811855	76.745	166	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACCUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	76.6835	179	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919455.1	s__UBA668 sp903919455	76.434	136	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.17	98.79	0.93	0.92	4	-
GCA_010024485.1	s__Casp-actino5 sp010024485	76.4147	82	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_013815505.1	s__JACDHN01 sp013815505	76.3341	114	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821025.1	s__JACDHN01 sp013821025	76.3127	124	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	97.95	97.95	0.71	0.71	2	-
GCF_009650215.1	s__Actinomarinicola tropica	75.9503	118	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	75.7421	89	1230	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:23:04,588] [INFO] GTDB search result was written to OceanDNA-b513/result_gtdb.tsv
[2023-03-16 01:23:04,588] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:23:04,589] [INFO] DFAST_QC result json was written to OceanDNA-b513/dqc_result.json
[2023-03-16 01:23:04,590] [INFO] DFAST_QC completed!
[2023-03-16 01:23:04,590] [INFO] Total running time: 0h1m52s