[2023-06-29 08:44:44,271] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:44,292] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:44,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference
[2023-06-29 08:44:46,978] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:46,979] [INFO] Task started: Prodigal
[2023-06-29 08:44:46,980] [INFO] Running command: gunzip -c /var/lib/cwl/stgdff2c5c3-bc0d-4fbf-ba40-cea466466285/GCA_020199775.1_ASM2019977v1_genomic.fna.gz | prodigal -d GCA_020199775.1_ASM2019977v1_genomic.fna/cds.fna -a GCA_020199775.1_ASM2019977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:45:03,009] [INFO] Task succeeded: Prodigal
[2023-06-29 08:45:03,010] [INFO] Task started: HMMsearch
[2023-06-29 08:45:03,010] [INFO] Running command: hmmsearch --tblout GCA_020199775.1_ASM2019977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference/reference_markers.hmm GCA_020199775.1_ASM2019977v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:45:03,339] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:45:03,340] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdff2c5c3-bc0d-4fbf-ba40-cea466466285/GCA_020199775.1_ASM2019977v1_genomic.fna.gz]
[2023-06-29 08:45:03,389] [INFO] Query marker FASTA was written to GCA_020199775.1_ASM2019977v1_genomic.fna/markers.fasta
[2023-06-29 08:45:03,390] [INFO] Task started: Blastn
[2023-06-29 08:45:03,390] [INFO] Running command: blastn -query GCA_020199775.1_ASM2019977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference/reference_markers.fasta -out GCA_020199775.1_ASM2019977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:04,084] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:04,089] [INFO] Selected 25 target genomes.
[2023-06-29 08:45:04,090] [INFO] Target genome list was writen to GCA_020199775.1_ASM2019977v1_genomic.fna/target_genomes.txt
[2023-06-29 08:45:04,097] [INFO] Task started: fastANI
[2023-06-29 08:45:04,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgdff2c5c3-bc0d-4fbf-ba40-cea466466285/GCA_020199775.1_ASM2019977v1_genomic.fna.gz --refList GCA_020199775.1_ASM2019977v1_genomic.fna/target_genomes.txt --output GCA_020199775.1_ASM2019977v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:45:25,180] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:25,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:45:25,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:45:25,201] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:45:25,201] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:45:25,202] [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
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9993	147	1932	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.9779	145	1932	95	below_threshold
Methylobacterium gnaphalii	strain=NBRC 107716	GCA_007992215.1	1010610	1010610	type	True	74.9642	50	1932	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	74.9043	95	1932	95	below_threshold
Methylobacterium gnaphalii	strain=DSM 24027	GCA_022179205.1	1010610	1010610	type	True	74.8956	52	1932	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	74.8462	84	1932	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	74.8302	101	1932	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.7764	107	1932	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	74.763	64	1932	95	below_threshold
Paraburkholderia phenazinium	strain=LMG 2247	GCA_900100735.1	60549	60549	type	True	74.7525	51	1932	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	74.7449	133	1932	95	below_threshold
Streptomyces varsoviensis	strain=NRRL ISP-5346	GCA_000718635.1	67373	67373	type	True	74.7441	132	1932	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	74.7256	55	1932	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.7141	95	1932	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	74.7069	111	1932	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	74.69	78	1932	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	74.6728	114	1932	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:45:25,204] [INFO] DFAST Taxonomy check result was written to GCA_020199775.1_ASM2019977v1_genomic.fna/tc_result.tsv
[2023-06-29 08:45:25,204] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:45:25,204] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:45:25,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference/checkm_data
[2023-06-29 08:45:25,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:45:25,258] [INFO] Task started: CheckM
[2023-06-29 08:45:25,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020199775.1_ASM2019977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020199775.1_ASM2019977v1_genomic.fna/checkm_input GCA_020199775.1_ASM2019977v1_genomic.fna/checkm_result
[2023-06-29 08:46:12,341] [INFO] Task succeeded: CheckM
[2023-06-29 08:46:12,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:46:12,369] [INFO] ===== Completeness check finished =====
[2023-06-29 08:46:12,370] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:46:12,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020199775.1_ASM2019977v1_genomic.fna/markers.fasta)
[2023-06-29 08:46:12,370] [INFO] Task started: Blastn
[2023-06-29 08:46:12,370] [INFO] Running command: blastn -query GCA_020199775.1_ASM2019977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d50e23c-9698-4208-9f87-3e7e538a8b8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_020199775.1_ASM2019977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:46:13,335] [INFO] Task succeeded: Blastn
[2023-06-29 08:46:13,340] [INFO] Selected 8 target genomes.
[2023-06-29 08:46:13,340] [INFO] Target genome list was writen to GCA_020199775.1_ASM2019977v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:46:13,354] [INFO] Task started: fastANI
[2023-06-29 08:46:13,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgdff2c5c3-bc0d-4fbf-ba40-cea466466285/GCA_020199775.1_ASM2019977v1_genomic.fna.gz --refList GCA_020199775.1_ASM2019977v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020199775.1_ASM2019977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:46:21,242] [INFO] Task succeeded: fastANI
[2023-06-29 08:46:21,252] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:46:21,252] [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_003222975.1	s__QHXN01 sp003222975	78.6729	623	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223935.1	s__QHXQ01 sp003223935	78.4735	604	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813825.1	s__JACCRA01 sp013813825	78.4242	334	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACCRA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242475.1	s__QHXN01 sp019242475	78.3898	657	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239425.1	s__QHXN01 sp019239425	78.318	714	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__QHXN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816505.1	s__JACDEG01 sp013816505	77.5338	415	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACDEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247865.1	s__JACMLC01 sp019247865	77.4907	300	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACMLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695245.1	s__JACCYN01 sp013695245	76.7966	209	1932	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__Pyrinomonadales;f__Pyrinomonadaceae;g__JACCYN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:46:21,255] [INFO] GTDB search result was written to GCA_020199775.1_ASM2019977v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:46:21,256] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:46:21,261] [INFO] DFAST_QC result json was written to GCA_020199775.1_ASM2019977v1_genomic.fna/dqc_result.json
[2023-06-29 08:46:21,262] [INFO] DFAST_QC completed!
[2023-06-29 08:46:21,262] [INFO] Total running time: 0h1m37s