[2023-06-29 00:46:46,323] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:46:46,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:46:46,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference
[2023-06-29 00:46:47,574] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:46:47,575] [INFO] Task started: Prodigal
[2023-06-29 00:46:47,576] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a4c25e9-ce98-4b8e-a613-9c70d33604d7/GCA_020401985.1_ASM2040198v1_genomic.fna.gz | prodigal -d GCA_020401985.1_ASM2040198v1_genomic.fna/cds.fna -a GCA_020401985.1_ASM2040198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:46:52,978] [INFO] Task succeeded: Prodigal
[2023-06-29 00:46:52,979] [INFO] Task started: HMMsearch
[2023-06-29 00:46:52,979] [INFO] Running command: hmmsearch --tblout GCA_020401985.1_ASM2040198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference/reference_markers.hmm GCA_020401985.1_ASM2040198v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:46:53,271] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:46:53,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6a4c25e9-ce98-4b8e-a613-9c70d33604d7/GCA_020401985.1_ASM2040198v1_genomic.fna.gz]
[2023-06-29 00:46:53,300] [INFO] Query marker FASTA was written to GCA_020401985.1_ASM2040198v1_genomic.fna/markers.fasta
[2023-06-29 00:46:53,301] [INFO] Task started: Blastn
[2023-06-29 00:46:53,301] [INFO] Running command: blastn -query GCA_020401985.1_ASM2040198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference/reference_markers.fasta -out GCA_020401985.1_ASM2040198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:46:54,141] [INFO] Task succeeded: Blastn
[2023-06-29 00:46:54,146] [INFO] Selected 18 target genomes.
[2023-06-29 00:46:54,146] [INFO] Target genome list was writen to GCA_020401985.1_ASM2040198v1_genomic.fna/target_genomes.txt
[2023-06-29 00:46:54,148] [INFO] Task started: fastANI
[2023-06-29 00:46:54,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a4c25e9-ce98-4b8e-a613-9c70d33604d7/GCA_020401985.1_ASM2040198v1_genomic.fna.gz --refList GCA_020401985.1_ASM2040198v1_genomic.fna/target_genomes.txt --output GCA_020401985.1_ASM2040198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:47:08,345] [INFO] Task succeeded: fastANI
[2023-06-29 00:47:08,346] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:47:08,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:47:08,362] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:47:08,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:47:08,362] [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
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	85.7934	491	636	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.6166	339	636	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.4103	316	636	95	below_threshold
Phenylobacterium hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	79.3285	300	636	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	79.0748	290	636	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	79.0568	303	636	95	below_threshold
Phenylobacterium haematophilum	strain=DSM 21793	GCA_014196295.1	98513	98513	type	True	78.8945	275	636	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	78.8261	288	636	95	below_threshold
Phenylobacterium deserti	strain=YIM 73061	GCA_003254705.1	1914756	1914756	type	True	78.484	214	636	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	78.1859	244	636	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	78.1544	210	636	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	78.1434	222	636	95	below_threshold
Brevundimonas vesicularis	strain=NBRC 12165	GCA_001592205.1	41276	41276	suspected-type	True	77.3	122	636	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.7632	93	636	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.5255	122	636	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.5106	100	636	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	76.2394	66	636	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.1665	95	636	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:47:08,365] [INFO] DFAST Taxonomy check result was written to GCA_020401985.1_ASM2040198v1_genomic.fna/tc_result.tsv
[2023-06-29 00:47:08,366] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:47:08,366] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:47:08,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference/checkm_data
[2023-06-29 00:47:08,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:47:08,396] [INFO] Task started: CheckM
[2023-06-29 00:47:08,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020401985.1_ASM2040198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020401985.1_ASM2040198v1_genomic.fna/checkm_input GCA_020401985.1_ASM2040198v1_genomic.fna/checkm_result
[2023-06-29 00:47:31,379] [INFO] Task succeeded: CheckM
[2023-06-29 00:47:31,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.77%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:47:31,405] [INFO] ===== Completeness check finished =====
[2023-06-29 00:47:31,406] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:47:31,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020401985.1_ASM2040198v1_genomic.fna/markers.fasta)
[2023-06-29 00:47:31,407] [INFO] Task started: Blastn
[2023-06-29 00:47:31,407] [INFO] Running command: blastn -query GCA_020401985.1_ASM2040198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28a23219-517b-486d-bfdb-d2f35f07804b/dqc_reference/reference_markers_gtdb.fasta -out GCA_020401985.1_ASM2040198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:47:32,798] [INFO] Task succeeded: Blastn
[2023-06-29 00:47:32,803] [INFO] Selected 14 target genomes.
[2023-06-29 00:47:32,803] [INFO] Target genome list was writen to GCA_020401985.1_ASM2040198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:47:32,805] [INFO] Task started: fastANI
[2023-06-29 00:47:32,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a4c25e9-ce98-4b8e-a613-9c70d33604d7/GCA_020401985.1_ASM2040198v1_genomic.fna.gz --refList GCA_020401985.1_ASM2040198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020401985.1_ASM2040198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:47:42,357] [INFO] Task succeeded: fastANI
[2023-06-29 00:47:42,374] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 00:47:42,374] [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_903842425.1	s__Phenylobacterium sp903842425	86.5931	400	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003150835.1	s__Phenylobacterium parvum	85.8163	490	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912465.1	s__Phenylobacterium sp903912465	83.8745	394	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903933475.1	s__Phenylobacterium sp903933475	83.7657	414	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.29	99.29	0.84	0.84	2	-
GCA_018001015.1	s__Phenylobacterium sp018001015	79.4588	295	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.74	99.70	0.93	0.91	3	-
GCA_013911965.1	s__Phenylobacterium sp013911965	79.4402	295	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_002363865.1	s__Phenylobacterium sp002363865	79.3498	278	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.98	99.98	0.95	0.91	3	-
GCA_017991675.1	s__Phenylobacterium sp017991675	79.0045	206	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799515.1	s__Phenylobacterium sp004799515	78.9176	291	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124325.1	s__Phenylobacterium sp016124325	78.5636	276	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418605.1	s__CAISGS01 sp017418605	78.4439	262	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136395.1	s__Phenylobacterium sp003136395	78.3314	242	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045195.1	s__Caulobacter soli	78.201	243	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931565.1	s__Caulobacter sp003931565	77.8139	253	636	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:47:42,378] [INFO] GTDB search result was written to GCA_020401985.1_ASM2040198v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:47:42,378] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:47:42,383] [INFO] DFAST_QC result json was written to GCA_020401985.1_ASM2040198v1_genomic.fna/dqc_result.json
[2023-06-29 00:47:42,384] [INFO] DFAST_QC completed!
[2023-06-29 00:47:42,384] [INFO] Total running time: 0h0m56s