[2023-06-29 13:07:26,163] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:07:26,165] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:07:26,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference
[2023-06-29 13:07:27,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:07:27,473] [INFO] Task started: Prodigal
[2023-06-29 13:07:27,473] [INFO] Running command: gunzip -c /var/lib/cwl/stge6d267dc-4c62-4d3b-a0ca-ce6d146593ed/GCA_021848485.1_ASM2184848v1_genomic.fna.gz | prodigal -d GCA_021848485.1_ASM2184848v1_genomic.fna/cds.fna -a GCA_021848485.1_ASM2184848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:07:37,948] [INFO] Task succeeded: Prodigal
[2023-06-29 13:07:37,949] [INFO] Task started: HMMsearch
[2023-06-29 13:07:37,949] [INFO] Running command: hmmsearch --tblout GCA_021848485.1_ASM2184848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference/reference_markers.hmm GCA_021848485.1_ASM2184848v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:07:38,225] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:07:38,226] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge6d267dc-4c62-4d3b-a0ca-ce6d146593ed/GCA_021848485.1_ASM2184848v1_genomic.fna.gz]
[2023-06-29 13:07:38,269] [INFO] Query marker FASTA was written to GCA_021848485.1_ASM2184848v1_genomic.fna/markers.fasta
[2023-06-29 13:07:38,270] [INFO] Task started: Blastn
[2023-06-29 13:07:38,270] [INFO] Running command: blastn -query GCA_021848485.1_ASM2184848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference/reference_markers.fasta -out GCA_021848485.1_ASM2184848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:07:39,283] [INFO] Task succeeded: Blastn
[2023-06-29 13:07:39,287] [INFO] Selected 26 target genomes.
[2023-06-29 13:07:39,288] [INFO] Target genome list was writen to GCA_021848485.1_ASM2184848v1_genomic.fna/target_genomes.txt
[2023-06-29 13:07:39,296] [INFO] Task started: fastANI
[2023-06-29 13:07:39,296] [INFO] Running command: fastANI --query /var/lib/cwl/stge6d267dc-4c62-4d3b-a0ca-ce6d146593ed/GCA_021848485.1_ASM2184848v1_genomic.fna.gz --refList GCA_021848485.1_ASM2184848v1_genomic.fna/target_genomes.txt --output GCA_021848485.1_ASM2184848v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:08:02,861] [INFO] Task succeeded: fastANI
[2023-06-29 13:08:02,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:08:02,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:08:02,881] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:08:02,881] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:08:02,881] [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
Terrihabitans soli	strain=IZ6	GCA_014191545.1	708113	708113	type	True	79.4691	489	1236	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	78.0557	306	1236	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.7763	236	1236	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	77.7678	308	1236	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.7264	302	1236	95	below_threshold
Bradyrhizobium quebecense	strain=66S1MB, /ecotype=symbiovar septentrionalis	GCA_013373795.3	2748629	2748629	type	True	77.6909	334	1236	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	77.645	240	1236	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	77.6046	295	1236	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	77.5815	258	1236	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	77.5303	314	1236	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	77.4767	278	1236	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	77.4734	275	1236	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	77.4405	265	1236	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	77.4117	205	1236	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.4093	349	1236	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	77.3967	319	1236	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	77.3951	234	1236	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.3891	271	1236	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	77.3721	259	1236	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.3652	223	1236	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	77.3375	209	1236	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.3349	305	1236	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	77.3136	300	1236	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	77.3045	302	1236	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	77.2373	232	1236	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	77.139	323	1236	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:08:02,884] [INFO] DFAST Taxonomy check result was written to GCA_021848485.1_ASM2184848v1_genomic.fna/tc_result.tsv
[2023-06-29 13:08:02,884] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:08:02,884] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:08:02,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference/checkm_data
[2023-06-29 13:08:02,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:08:02,930] [INFO] Task started: CheckM
[2023-06-29 13:08:02,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021848485.1_ASM2184848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021848485.1_ASM2184848v1_genomic.fna/checkm_input GCA_021848485.1_ASM2184848v1_genomic.fna/checkm_result
[2023-06-29 13:08:36,374] [INFO] Task succeeded: CheckM
[2023-06-29 13:08:36,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:08:36,398] [INFO] ===== Completeness check finished =====
[2023-06-29 13:08:36,398] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:08:36,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021848485.1_ASM2184848v1_genomic.fna/markers.fasta)
[2023-06-29 13:08:36,399] [INFO] Task started: Blastn
[2023-06-29 13:08:36,399] [INFO] Running command: blastn -query GCA_021848485.1_ASM2184848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg012e0e41-1266-4688-ad15-5c2d2d41d5c4/dqc_reference/reference_markers_gtdb.fasta -out GCA_021848485.1_ASM2184848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:08:38,167] [INFO] Task succeeded: Blastn
[2023-06-29 13:08:38,172] [INFO] Selected 18 target genomes.
[2023-06-29 13:08:38,173] [INFO] Target genome list was writen to GCA_021848485.1_ASM2184848v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:08:38,184] [INFO] Task started: fastANI
[2023-06-29 13:08:38,185] [INFO] Running command: fastANI --query /var/lib/cwl/stge6d267dc-4c62-4d3b-a0ca-ce6d146593ed/GCA_021848485.1_ASM2184848v1_genomic.fna.gz --refList GCA_021848485.1_ASM2184848v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021848485.1_ASM2184848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:08:53,639] [INFO] Task succeeded: fastANI
[2023-06-29 13:08:53,667] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:08:53,668] [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_003347645.1	s__Ga0077545 sp003347645	99.9815	1215	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014191545.1	s__Ga0077545 sp014191545	79.4631	489	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464335.1	s__Ga0077545 sp001464335	79.1958	489	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473415.1	s__Bosea sp900473415	77.966	313	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185715.1	s__Bosea sp900185715	77.9576	331	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	77.9322	327	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	77.9261	308	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764485.1	s__Bosea sp011764485	77.7698	305	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009910705.1	s__Microvirga sp009910705	77.6621	217	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001556025.1	s__Bosea sp001556025	77.6235	285	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	77.6147	276	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCF_003046185.1	s__Phreatobacter oligotrophus	77.5937	296	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	77.4621	276	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415845.1	s__Rhodopseudomonas palustris_F	77.3957	268	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	97.90	97.49	0.94	0.92	8	-
GCF_016613415.1	s__Methylobacterium ajmalii	77.395	320	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	-
GCF_016653355.1	s__Rhodoplanes elegans	77.3445	304	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_005871085.1	s__Xanthobacter autotrophicus_A	77.3375	209	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667445.1	s__Xanthobacter tagetidis	77.317	301	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 13:08:53,670] [INFO] GTDB search result was written to GCA_021848485.1_ASM2184848v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:08:53,670] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:08:53,675] [INFO] DFAST_QC result json was written to GCA_021848485.1_ASM2184848v1_genomic.fna/dqc_result.json
[2023-06-29 13:08:53,675] [INFO] DFAST_QC completed!
[2023-06-29 13:08:53,676] [INFO] Total running time: 0h1m28s