[2024-01-24 13:58:55,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference
[2024-01-24 13:58:56,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:56,901] [INFO] Task started: Prodigal
[2024-01-24 13:58:56,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg005289cf-9fcb-4eb6-adc2-e14e55fab67c/GCF_009664975.1_ASM966497v1_genomic.fna.gz | prodigal -d GCF_009664975.1_ASM966497v1_genomic.fna/cds.fna -a GCF_009664975.1_ASM966497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:15,453] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:15,454] [INFO] Task started: HMMsearch
[2024-01-24 13:59:15,454] [INFO] Running command: hmmsearch --tblout GCF_009664975.1_ASM966497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference/reference_markers.hmm GCF_009664975.1_ASM966497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:15,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:15,752] [INFO] Found 6/6 markers.
[2024-01-24 13:59:15,808] [INFO] Query marker FASTA was written to GCF_009664975.1_ASM966497v1_genomic.fna/markers.fasta
[2024-01-24 13:59:15,808] [INFO] Task started: Blastn
[2024-01-24 13:59:15,808] [INFO] Running command: blastn -query GCF_009664975.1_ASM966497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference/reference_markers.fasta -out GCF_009664975.1_ASM966497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:16,401] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:16,404] [INFO] Selected 29 target genomes.
[2024-01-24 13:59:16,404] [INFO] Target genome list was writen to GCF_009664975.1_ASM966497v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:16,413] [INFO] Task started: fastANI
[2024-01-24 13:59:16,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg005289cf-9fcb-4eb6-adc2-e14e55fab67c/GCF_009664975.1_ASM966497v1_genomic.fna.gz --refList GCF_009664975.1_ASM966497v1_genomic.fna/target_genomes.txt --output GCF_009664975.1_ASM966497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:49,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:49,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:49,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:49,568] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:49,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:49,569] [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
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	79.8669	752	2344	95	below_threshold
Paenibacillus sonchi	strain=X19-5	GCA_000316285.1	373687	373687	type	True	79.729	664	2344	95	below_threshold
Paenibacillus etheri	strain=SH7	GCA_001012825.2	1306852	1306852	type	True	79.726	731	2344	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	79.7098	804	2344	95	below_threshold
Paenibacillus donghaensis	strain=KCTC 13049	GCA_002192415.1	414771	414771	type	True	79.6668	811	2344	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	79.663	775	2344	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	79.6592	744	2344	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	79.5894	822	2344	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.5868	745	2344	95	below_threshold
Paenibacillus jilunlii	strain=CGMCC 1.10239	GCA_900102965.1	682956	682956	type	True	79.466	805	2344	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	79.4644	838	2344	95	below_threshold
Paenibacillus jilunlii	strain=DSM 23019	GCA_001546055.1	682956	682956	type	True	79.4249	796	2344	95	below_threshold
Paenibacillus graminis	strain=DSM 15220	GCA_000758705.1	189425	189425	type	True	79.4159	794	2344	95	below_threshold
Paenibacillus wynnii	strain=DSM 18334	GCA_000757885.1	268407	268407	type	True	79.4099	725	2344	95	below_threshold
Paenibacillus graminis	strain=RSA19	GCA_000520655.1	189425	189425	type	True	79.368	679	2344	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	79.3104	792	2344	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	79.2447	728	2344	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.2081	619	2344	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	77.8954	332	2344	95	below_threshold
Paenibacillus apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	77.627	342	2344	95	below_threshold
Paenibacillus stellifer	strain=DSM 14472	GCA_000758685.1	169760	169760	type	True	77.5188	294	2344	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	77.4908	116	2344	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	77.3201	107	2344	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	77.2797	116	2344	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	77.0185	99	2344	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	76.7646	98	2344	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.4196	61	2344	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	76.045	64	2344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,570] [INFO] DFAST Taxonomy check result was written to GCF_009664975.1_ASM966497v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:49,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:49,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:49,571] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference/checkm_data
[2024-01-24 13:59:49,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:49,635] [INFO] Task started: CheckM
[2024-01-24 13:59:49,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009664975.1_ASM966497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009664975.1_ASM966497v1_genomic.fna/checkm_input GCF_009664975.1_ASM966497v1_genomic.fna/checkm_result
[2024-01-24 14:00:45,227] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:45,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:45,249] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:45,249] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:45,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009664975.1_ASM966497v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:45,250] [INFO] Task started: Blastn
[2024-01-24 14:00:45,250] [INFO] Running command: blastn -query GCF_009664975.1_ASM966497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg605a72d6-9a11-4610-844e-24366c53321a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009664975.1_ASM966497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:46,067] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:46,071] [INFO] Selected 19 target genomes.
[2024-01-24 14:00:46,071] [INFO] Target genome list was writen to GCF_009664975.1_ASM966497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:46,089] [INFO] Task started: fastANI
[2024-01-24 14:00:46,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg005289cf-9fcb-4eb6-adc2-e14e55fab67c/GCF_009664975.1_ASM966497v1_genomic.fna.gz --refList GCF_009664975.1_ASM966497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009664975.1_ASM966497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:10,208] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:10,223] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:10,223] [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
GCF_009664975.1	s__Paenibacillus sp009664975	100.0	2340	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000758725.1	s__Paenibacillus odorifer	79.8728	752	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
GCF_001909055.1	s__Paenibacillus helianthi	79.7639	842	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.61	95.31	0.90	0.83	4	-
GCF_001012825.1	s__Paenibacillus etheri	79.7186	733	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758545.1	s__Paenibacillus sp000758545	79.6899	749	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.87	97.65	0.91	0.90	4	-
GCF_002192415.1	s__Paenibacillus donghaensis	79.6753	809	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758665.1	s__Paenibacillus borealis	79.6101	818	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438345.1	s__Paenibacillus sp002438345	79.5646	650	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758585.1	s__Paenibacillus sp000758585	79.5468	741	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.21	98.21	0.91	0.91	2	-
GCF_900102965.1	s__Paenibacillus jilunlii	79.47	805	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.98	99.98	1.00	0.99	3	-
GCF_002264395.1	s__Paenibacillus sp002264395	79.4545	706	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
GCF_000758705.1	s__Paenibacillus graminis	79.4288	792	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000757885.1	s__Paenibacillus wynnii	79.4034	727	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018966525.1	s__Paenibacillus sophorae	77.6112	381	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000758685.1	s__Paenibacillus stellifer	77.5286	293	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333375.1	s__Paenibacillus cookii	77.3524	97	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
GCF_014639235.1	s__Paenibacillus silvae	77.2658	106	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	76.7229	99	2344	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:10,225] [INFO] GTDB search result was written to GCF_009664975.1_ASM966497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:10,225] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:10,230] [INFO] DFAST_QC result json was written to GCF_009664975.1_ASM966497v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:10,230] [INFO] DFAST_QC completed!
[2024-01-24 14:01:10,230] [INFO] Total running time: 0h2m15s