[2024-01-24 11:19:48,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:48,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:48,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference
[2024-01-24 11:19:50,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,112] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5cac16e-229e-4f5c-bf90-ee26fa854768/GCF_022898935.1_ASM2289893v1_genomic.fna.gz | prodigal -d GCF_022898935.1_ASM2289893v1_genomic.fna/cds.fna -a GCF_022898935.1_ASM2289893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:05,648] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:05,648] [INFO] Task started: HMMsearch
[2024-01-24 11:20:05,649] [INFO] Running command: hmmsearch --tblout GCF_022898935.1_ASM2289893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference/reference_markers.hmm GCF_022898935.1_ASM2289893v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:05,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:05,977] [INFO] Found 6/6 markers.
[2024-01-24 11:20:06,035] [INFO] Query marker FASTA was written to GCF_022898935.1_ASM2289893v1_genomic.fna/markers.fasta
[2024-01-24 11:20:06,035] [INFO] Task started: Blastn
[2024-01-24 11:20:06,035] [INFO] Running command: blastn -query GCF_022898935.1_ASM2289893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference/reference_markers.fasta -out GCF_022898935.1_ASM2289893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:06,638] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:06,641] [INFO] Selected 25 target genomes.
[2024-01-24 11:20:06,641] [INFO] Target genome list was writen to GCF_022898935.1_ASM2289893v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:06,654] [INFO] Task started: fastANI
[2024-01-24 11:20:06,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5cac16e-229e-4f5c-bf90-ee26fa854768/GCF_022898935.1_ASM2289893v1_genomic.fna.gz --refList GCF_022898935.1_ASM2289893v1_genomic.fna/target_genomes.txt --output GCF_022898935.1_ASM2289893v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:31,195] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:31,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:31,196] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:31,215] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:31,215] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:31,216] [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 dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	83.085	1086	1966	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	82.1958	970	1966	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	79.1557	527	1966	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	78.384	292	1966	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_001315125.1	669461	669461	type	True	78.3624	293	1966	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	78.3017	281	1966	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	78.1053	289	1966	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	77.9537	179	1966	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.7266	171	1966	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.726	158	1966	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	77.674	238	1966	95	below_threshold
Paenibacillus azotifigens	strain=LMG 29963	GCA_008635805.1	2047734	2047734	type	True	77.6504	205	1966	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.648	182	1966	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	77.6233	188	1966	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	77.5677	202	1966	95	below_threshold
Paenibacillus pinistramenti	strain=ASL46	GCA_005869875.1	1768003	1768003	type	True	77.5675	163	1966	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.4684	212	1966	95	below_threshold
Paenibacillus typhae	strain=CGMCC 1.11012	GCA_900099765.1	1174501	1174501	type	True	77.3836	194	1966	95	below_threshold
Paenibacillus physcomitrellae	strain=XB	GCA_002240225.1	1619311	1619311	type	True	77.3782	189	1966	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	77.3743	195	1966	95	below_threshold
Paenibacillus physcomitrellae	strain=CGMCC 1.15044	GCA_014640575.1	1619311	1619311	type	True	77.2831	187	1966	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.2222	177	1966	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	77.1298	199	1966	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	77.1149	217	1966	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.6853	194	1966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:31,218] [INFO] DFAST Taxonomy check result was written to GCF_022898935.1_ASM2289893v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:31,219] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:31,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:31,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference/checkm_data
[2024-01-24 11:20:31,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:31,282] [INFO] Task started: CheckM
[2024-01-24 11:20:31,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022898935.1_ASM2289893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022898935.1_ASM2289893v1_genomic.fna/checkm_input GCF_022898935.1_ASM2289893v1_genomic.fna/checkm_result
[2024-01-24 11:21:18,761] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:18,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:18,785] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:18,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:18,786] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022898935.1_ASM2289893v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:18,786] [INFO] Task started: Blastn
[2024-01-24 11:21:18,786] [INFO] Running command: blastn -query GCF_022898935.1_ASM2289893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c8b6ea-74bb-4f8f-b348-19ff22768655/dqc_reference/reference_markers_gtdb.fasta -out GCF_022898935.1_ASM2289893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:19,598] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:19,603] [INFO] Selected 9 target genomes.
[2024-01-24 11:21:19,603] [INFO] Target genome list was writen to GCF_022898935.1_ASM2289893v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:19,611] [INFO] Task started: fastANI
[2024-01-24 11:21:19,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5cac16e-229e-4f5c-bf90-ee26fa854768/GCF_022898935.1_ASM2289893v1_genomic.fna.gz --refList GCF_022898935.1_ASM2289893v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022898935.1_ASM2289893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:29,895] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:29,906] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:29,906] [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_009807035.1	s__Paenibacillus sp009807035	83.7105	1119	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916975.1	s__Paenibacillus dokdonensis	83.0771	1087	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403225.1	s__Paenibacillus sp018403225	82.9358	1092	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001045.1	s__Paenibacillus chibensis	82.1699	972	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333315.1	s__Paenibacillus azoreducens	81.4326	972	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_018333375.1	s__Paenibacillus cookii	80.6537	787	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
GCF_001373415.1	s__Paenibacillus dakarensis	77.937	180	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002264395.1	s__Paenibacillus sp002264395	77.5202	144	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
GCF_000758585.1	s__Paenibacillus sp000758585	77.4802	165	1966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.21	98.21	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:29,907] [INFO] GTDB search result was written to GCF_022898935.1_ASM2289893v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:29,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:29,912] [INFO] DFAST_QC result json was written to GCF_022898935.1_ASM2289893v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:29,912] [INFO] DFAST_QC completed!
[2024-01-24 11:21:29,912] [INFO] Total running time: 0h1m41s