[2023-03-18 06:30:24,814] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,817] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,817] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference
[2023-03-18 06:30:25,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,962] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,962] [INFO] Running command: cat /var/lib/cwl/stg5cdad0ef-6b63-4cf5-9142-a60ed34e8949/OceanDNA-b520.fa | prodigal -d OceanDNA-b520/cds.fna -a OceanDNA-b520/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:35,795] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:35,796] [INFO] Task started: HMMsearch
[2023-03-18 06:30:35,796] [INFO] Running command: hmmsearch --tblout OceanDNA-b520/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference/reference_markers.hmm OceanDNA-b520/protein.faa > /dev/null
[2023-03-18 06:30:35,943] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:35,944] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5cdad0ef-6b63-4cf5-9142-a60ed34e8949/OceanDNA-b520.fa]
[2023-03-18 06:30:35,984] [INFO] Query marker FASTA was written to OceanDNA-b520/markers.fasta
[2023-03-18 06:30:35,985] [INFO] Task started: Blastn
[2023-03-18 06:30:35,985] [INFO] Running command: blastn -query OceanDNA-b520/markers.fasta -db /var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference/reference_markers.fasta -out OceanDNA-b520/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:36,601] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:36,608] [INFO] Selected 23 target genomes.
[2023-03-18 06:30:36,608] [INFO] Target genome list was writen to OceanDNA-b520/target_genomes.txt
[2023-03-18 06:30:36,672] [INFO] Task started: fastANI
[2023-03-18 06:30:36,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cdad0ef-6b63-4cf5-9142-a60ed34e8949/OceanDNA-b520.fa --refList OceanDNA-b520/target_genomes.txt --output OceanDNA-b520/fastani_result.tsv --threads 1
[2023-03-18 06:30:59,163] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:59,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:59,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:59,174] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:59,174] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:30:59,174] [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	77.1326	138	497	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.0622	166	497	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.681	109	497	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6475	123	497	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.5914	104	497	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	75.4552	60	497	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	75.4132	77	497	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	75.3768	74	497	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	75.2736	85	497	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	75.2245	52	497	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	75.198	51	497	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	75.1977	51	497	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	75.1777	69	497	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	75.131	71	497	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	75.0986	54	497	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.011	64	497	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:30:59,176] [INFO] DFAST Taxonomy check result was written to OceanDNA-b520/tc_result.tsv
[2023-03-18 06:30:59,176] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:59,176] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:59,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference/checkm_data
[2023-03-18 06:30:59,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:59,204] [INFO] Task started: CheckM
[2023-03-18 06:30:59,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b520/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b520/checkm_input OceanDNA-b520/checkm_result
[2023-03-18 06:31:35,804] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:35,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:35,905] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:35,905] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:35,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b520/markers.fasta)
[2023-03-18 06:31:35,906] [INFO] Task started: Blastn
[2023-03-18 06:31:35,906] [INFO] Running command: blastn -query OceanDNA-b520/markers.fasta -db /var/lib/cwl/stgb0b0c464-b019-4da5-8537-f488565e6e8e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b520/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:36,832] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:36,852] [INFO] Selected 18 target genomes.
[2023-03-18 06:31:36,852] [INFO] Target genome list was writen to OceanDNA-b520/target_genomes_gtdb.txt
[2023-03-18 06:31:37,063] [INFO] Task started: fastANI
[2023-03-18 06:31:37,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cdad0ef-6b63-4cf5-9142-a60ed34e8949/OceanDNA-b520.fa --refList OceanDNA-b520/target_genomes_gtdb.txt --output OceanDNA-b520/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:47,095] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:47,105] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:31:47,105] [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_009920715.1	s__UBA2093 sp009920715	98.8455	400	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	97.14	95.07	0.80	0.77	6	conclusive
GCA_005788205.1	s__UBA2093 sp005788205	83.2263	290	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870775.1	s__UBA2093 sp016870775	78.7698	208	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA2093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969685.1	s__UBA3006 sp018969685	77.8355	148	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA3006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	77.7543	192	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871355.1	s__Casp-actino8 sp016871355	77.5674	98	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	77.3575	162	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.172	136	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009919275.1	s__F1-20-MAGs119 sp009919275	77.1615	97	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__F1-20-MAGs119	95.0	99.53	99.53	0.87	0.87	2	-
GCF_003426815.1	s__Desertimonas flava	77.0495	168	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013815505.1	s__JACDHN01 sp013815505	76.8932	69	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	76.7948	104	497	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_016716005.1	s__JADJXE01 sp016716005	76.7085	112	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	76.5078	76	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	76.2826	59	497	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	75.4034	78	497	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:47,113] [INFO] GTDB search result was written to OceanDNA-b520/result_gtdb.tsv
[2023-03-18 06:31:47,124] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:47,137] [INFO] DFAST_QC result json was written to OceanDNA-b520/dqc_result.json
[2023-03-18 06:31:47,137] [INFO] DFAST_QC completed!
[2023-03-18 06:31:47,137] [INFO] Total running time: 0h1m22s