[2023-06-28 15:41:48,073] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:41:48,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:41:48,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference
[2023-06-28 15:41:49,259] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:41:49,259] [INFO] Task started: Prodigal
[2023-06-28 15:41:49,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg282ad221-1d60-4487-be4b-933920f95159/GCA_020847555.1_ASM2084755v1_genomic.fna.gz | prodigal -d GCA_020847555.1_ASM2084755v1_genomic.fna/cds.fna -a GCA_020847555.1_ASM2084755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:42:04,618] [INFO] Task succeeded: Prodigal
[2023-06-28 15:42:04,618] [INFO] Task started: HMMsearch
[2023-06-28 15:42:04,618] [INFO] Running command: hmmsearch --tblout GCA_020847555.1_ASM2084755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference/reference_markers.hmm GCA_020847555.1_ASM2084755v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:42:04,879] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:42:04,880] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg282ad221-1d60-4487-be4b-933920f95159/GCA_020847555.1_ASM2084755v1_genomic.fna.gz]
[2023-06-28 15:42:04,932] [INFO] Query marker FASTA was written to GCA_020847555.1_ASM2084755v1_genomic.fna/markers.fasta
[2023-06-28 15:42:04,933] [INFO] Task started: Blastn
[2023-06-28 15:42:04,933] [INFO] Running command: blastn -query GCA_020847555.1_ASM2084755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference/reference_markers.fasta -out GCA_020847555.1_ASM2084755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:42:05,691] [INFO] Task succeeded: Blastn
[2023-06-28 15:42:05,695] [INFO] Selected 20 target genomes.
[2023-06-28 15:42:05,696] [INFO] Target genome list was writen to GCA_020847555.1_ASM2084755v1_genomic.fna/target_genomes.txt
[2023-06-28 15:42:05,697] [INFO] Task started: fastANI
[2023-06-28 15:42:05,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg282ad221-1d60-4487-be4b-933920f95159/GCA_020847555.1_ASM2084755v1_genomic.fna.gz --refList GCA_020847555.1_ASM2084755v1_genomic.fna/target_genomes.txt --output GCA_020847555.1_ASM2084755v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:42:28,133] [INFO] Task succeeded: fastANI
[2023-06-28 15:42:28,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:42:28,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:42:28,148] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:42:28,149] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:42:28,149] [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
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	76.1057	459	1878	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	76.0306	285	1878	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	76.0294	271	1878	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	75.9848	290	1878	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	75.981	291	1878	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	75.8781	261	1878	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.5914	181	1878	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.5504	263	1878	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	74.8705	182	1878	95	below_threshold
Jatrophihabitans endophyticus	strain=DSM 45627	GCA_900129455.1	1206085	1206085	type	True	74.7743	145	1878	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	74.7449	194	1878	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	74.7409	175	1878	95	below_threshold
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	74.7331	209	1878	95	below_threshold
Streptomyces albidoflavus	strain=DSM 40455	GCA_004195735.1	1886	1886	type	True	74.7025	184	1878	95	below_threshold
Nesterenkonia halophila	strain=DSM 16378	GCA_009467795.1	302044	302044	type	True	74.696	70	1878	95	below_threshold
Georgenia thermotolerans	strain=NBRC 104148	GCA_009193185.1	527326	527326	type	True	74.6867	155	1878	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	74.661	177	1878	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	74.6322	55	1878	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:42:28,151] [INFO] DFAST Taxonomy check result was written to GCA_020847555.1_ASM2084755v1_genomic.fna/tc_result.tsv
[2023-06-28 15:42:28,151] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:42:28,152] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:42:28,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference/checkm_data
[2023-06-28 15:42:28,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:42:28,212] [INFO] Task started: CheckM
[2023-06-28 15:42:28,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020847555.1_ASM2084755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020847555.1_ASM2084755v1_genomic.fna/checkm_input GCA_020847555.1_ASM2084755v1_genomic.fna/checkm_result
[2023-06-28 15:43:12,645] [INFO] Task succeeded: CheckM
[2023-06-28 15:43:12,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:43:12,669] [INFO] ===== Completeness check finished =====
[2023-06-28 15:43:12,669] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:43:12,669] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020847555.1_ASM2084755v1_genomic.fna/markers.fasta)
[2023-06-28 15:43:12,669] [INFO] Task started: Blastn
[2023-06-28 15:43:12,670] [INFO] Running command: blastn -query GCA_020847555.1_ASM2084755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c5d68f4-3047-40d5-bd9f-56546b143630/dqc_reference/reference_markers_gtdb.fasta -out GCA_020847555.1_ASM2084755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:43:13,774] [INFO] Task succeeded: Blastn
[2023-06-28 15:43:13,777] [INFO] Selected 22 target genomes.
[2023-06-28 15:43:13,777] [INFO] Target genome list was writen to GCA_020847555.1_ASM2084755v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:43:13,782] [INFO] Task started: fastANI
[2023-06-28 15:43:13,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg282ad221-1d60-4487-be4b-933920f95159/GCA_020847555.1_ASM2084755v1_genomic.fna.gz --refList GCA_020847555.1_ASM2084755v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020847555.1_ASM2084755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:43:39,771] [INFO] Task succeeded: fastANI
[2023-06-28 15:43:39,789] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:43:39,789] [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_016873095.1	s__VGYC01 sp016873095	76.8414	332	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__VGYC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016177925.1	s__JACOUH01 sp016177925	76.6143	400	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__JACOUH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200155.1	s__SIAQ01 sp016200155	76.5487	196	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692065.1	s__SIAQ01 sp009692065	76.3974	230	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404095.1	s__UBA4732 sp002404095	76.3376	251	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA4732	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195405.1	s__JACPZP01 sp016195405	76.2659	209	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__JACPZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	76.1617	448	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308215.1	s__Urbifossiella sp017308215	76.1539	464	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013128195.2	s__Gemmata tundricola	76.039	327	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	75.8628	297	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191165.1	s__SIAQ01 sp016191165	75.8188	216	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065895.1	s__Paludisphaera sp011065895	75.6373	176	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331615.1	s__DSRJ01 sp011331615	75.6165	99	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__DSRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	75.5615	260	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	75.1562	113	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360685.1	s__JABWBD01 sp013360685	75.0216	86	1878	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	74.8617	57	1878	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000444875.1	s__Streptomyces collinus_A	74.7755	182	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.10	97.10	0.84	0.84	2	-
GCF_014648855.1	s__Streptomyces parvulus	74.7514	190	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_018274385.1	s__Catenulispora sp018274385	74.7341	208	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.51	99.51	0.94	0.94	2	-
GCF_003002095.1	s__Allonocardiopsis opalescens	74.7255	233	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allonocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220985.1	s__Nesterenkonia sp000220985	74.7006	69	1878	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Nesterenkonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:43:39,791] [INFO] GTDB search result was written to GCA_020847555.1_ASM2084755v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:43:39,792] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:43:39,796] [INFO] DFAST_QC result json was written to GCA_020847555.1_ASM2084755v1_genomic.fna/dqc_result.json
[2023-06-28 15:43:39,796] [INFO] DFAST_QC completed!
[2023-06-28 15:43:39,796] [INFO] Total running time: 0h1m52s