[2023-06-28 21:51:38,437] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:51:38,444] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:51:38,444] [INFO] DQC Reference Directory: /var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference
[2023-06-28 21:51:40,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:51:40,457] [INFO] Task started: Prodigal
[2023-06-28 21:51:40,458] [INFO] Running command: gunzip -c /var/lib/cwl/stg87534c50-0404-40f0-8a0e-542d4c7020ee/GCA_027431855.1_ASM2743185v1_genomic.fna.gz | prodigal -d GCA_027431855.1_ASM2743185v1_genomic.fna/cds.fna -a GCA_027431855.1_ASM2743185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:51:46,297] [INFO] Task succeeded: Prodigal
[2023-06-28 21:51:46,298] [INFO] Task started: HMMsearch
[2023-06-28 21:51:46,298] [INFO] Running command: hmmsearch --tblout GCA_027431855.1_ASM2743185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference/reference_markers.hmm GCA_027431855.1_ASM2743185v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:51:46,536] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:51:46,538] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87534c50-0404-40f0-8a0e-542d4c7020ee/GCA_027431855.1_ASM2743185v1_genomic.fna.gz]
[2023-06-28 21:51:46,566] [INFO] Query marker FASTA was written to GCA_027431855.1_ASM2743185v1_genomic.fna/markers.fasta
[2023-06-28 21:51:46,566] [INFO] Task started: Blastn
[2023-06-28 21:51:46,566] [INFO] Running command: blastn -query GCA_027431855.1_ASM2743185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference/reference_markers.fasta -out GCA_027431855.1_ASM2743185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:51:47,301] [INFO] Task succeeded: Blastn
[2023-06-28 21:51:47,306] [INFO] Selected 26 target genomes.
[2023-06-28 21:51:47,307] [INFO] Target genome list was writen to GCA_027431855.1_ASM2743185v1_genomic.fna/target_genomes.txt
[2023-06-28 21:51:47,310] [INFO] Task started: fastANI
[2023-06-28 21:51:47,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg87534c50-0404-40f0-8a0e-542d4c7020ee/GCA_027431855.1_ASM2743185v1_genomic.fna.gz --refList GCA_027431855.1_ASM2743185v1_genomic.fna/target_genomes.txt --output GCA_027431855.1_ASM2743185v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:52:03,398] [INFO] Task succeeded: fastANI
[2023-06-28 21:52:03,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:52:03,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:52:03,420] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:52:03,420] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 21:52:03,420] [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 hankyongense	strain=HKS-05	GCA_003254505.1	1813876	1813876	type	True	77.1051	161	641	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	77.0715	149	641	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	77.0127	159	641	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	76.9195	123	641	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	76.8768	100	641	95	below_threshold
Caulobacter mirabilis	strain=FWC 38	GCA_002749615.1	69666	69666	type	True	76.7236	141	641	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.6905	176	641	95	below_threshold
Phenylobacterium kunshanense	strain=BUT-10	GCA_003254525.1	1445034	1445034	type	True	76.6272	138	641	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	76.617	127	641	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	76.5625	127	641	95	below_threshold
Brevundimonas aveniformis	strain=DSM 17977	GCA_000428765.1	370977	370977	type	True	76.5373	64	641	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	76.3828	134	641	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	76.3693	132	641	95	below_threshold
Brevundimonas aurantiaca	strain=DSM 4731	GCA_014199955.1	74316	74316	type	True	76.2828	96	641	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	76.2754	94	641	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	75.9507	52	641	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	75.5504	67	641	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.4151	78	641	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.363	55	641	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.0962	53	641	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.0944	54	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 21:52:03,422] [INFO] DFAST Taxonomy check result was written to GCA_027431855.1_ASM2743185v1_genomic.fna/tc_result.tsv
[2023-06-28 21:52:03,423] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:52:03,423] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:52:03,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference/checkm_data
[2023-06-28 21:52:03,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:52:03,456] [INFO] Task started: CheckM
[2023-06-28 21:52:03,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027431855.1_ASM2743185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027431855.1_ASM2743185v1_genomic.fna/checkm_input GCA_027431855.1_ASM2743185v1_genomic.fna/checkm_result
[2023-06-28 21:52:27,076] [INFO] Task succeeded: CheckM
[2023-06-28 21:52:27,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:52:27,101] [INFO] ===== Completeness check finished =====
[2023-06-28 21:52:27,101] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:52:27,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027431855.1_ASM2743185v1_genomic.fna/markers.fasta)
[2023-06-28 21:52:27,102] [INFO] Task started: Blastn
[2023-06-28 21:52:27,102] [INFO] Running command: blastn -query GCA_027431855.1_ASM2743185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb55372ec-4082-4074-a0b3-a0d04a7575b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_027431855.1_ASM2743185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:52:28,353] [INFO] Task succeeded: Blastn
[2023-06-28 21:52:28,359] [INFO] Selected 18 target genomes.
[2023-06-28 21:52:28,359] [INFO] Target genome list was writen to GCA_027431855.1_ASM2743185v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:52:28,366] [INFO] Task started: fastANI
[2023-06-28 21:52:28,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg87534c50-0404-40f0-8a0e-542d4c7020ee/GCA_027431855.1_ASM2743185v1_genomic.fna.gz --refList GCA_027431855.1_ASM2743185v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027431855.1_ASM2743185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:52:39,665] [INFO] Task succeeded: fastANI
[2023-06-28 21:52:39,681] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:52:39,681] [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_013815405.1	s__Palsa-881 sp013815405	77.7215	131	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241335.1	s__Palsa-881 sp018241335	77.4963	179	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911965.1	s__Phenylobacterium sp013911965	77.3171	159	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	98.20	98.20	0.93	0.93	2	-
GCA_003136615.1	s__Palsa-881 sp003136615	77.313	183	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.34	99.34	0.88	0.88	2	-
GCA_903870555.1	s__Palsa-881 sp903870555	77.1652	152	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.20	99.20	0.85	0.85	2	-
GCF_016467375.1	s__Caulobacter sp016467375	77.1538	130	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903923135.1	s__Palsa-881 sp903923135	77.1294	196	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.95	99.94	0.96	0.95	3	-
GCA_019232665.1	s__Palsa-881 sp019232665	77.1128	174	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745545.1	s__Caulobacter henricii_C	77.1037	135	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.38	99.38	0.95	0.95	2	-
GCA_903872075.1	s__Palsa-881 sp903872075	77.0479	171	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	99.76	99.48	0.94	0.93	7	-
GCA_004799395.1	s__Phenylobacterium sp004799395	76.9189	137	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161535.1	s__Palsa-881 sp003161535	76.6516	98	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297125.1	s__Phenylobacterium sp004297125	76.5984	151	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744465.1	s__Caulobacter henricii_A	76.5944	134	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429025.1	s__Phenylobacterium sp001429025	76.5927	123	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	99.02	99.02	0.94	0.94	2	-
GCF_016135805.1	s__Caulobacter hibisci	76.5625	127	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842425.1	s__Phenylobacterium sp903842425	76.5011	98	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903851655.1	s__CAIMFV01 sp903851655	76.4705	137	641	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAIMFV01	95.0	99.52	99.51	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-28 21:52:39,683] [INFO] GTDB search result was written to GCA_027431855.1_ASM2743185v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:52:39,684] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:52:39,688] [INFO] DFAST_QC result json was written to GCA_027431855.1_ASM2743185v1_genomic.fna/dqc_result.json
[2023-06-28 21:52:39,688] [INFO] DFAST_QC completed!
[2023-06-28 21:52:39,688] [INFO] Total running time: 0h1m1s