[2024-01-24 12:40:51,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:51,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:51,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference
[2024-01-24 12:40:52,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:52,278] [INFO] Task started: Prodigal
[2024-01-24 12:40:52,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd009f62-ffb0-4b6e-8b58-9623eb5778fa/GCF_024721975.1_ASM2472197v1_genomic.fna.gz | prodigal -d GCF_024721975.1_ASM2472197v1_genomic.fna/cds.fna -a GCF_024721975.1_ASM2472197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:04,245] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:04,245] [INFO] Task started: HMMsearch
[2024-01-24 12:41:04,245] [INFO] Running command: hmmsearch --tblout GCF_024721975.1_ASM2472197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference/reference_markers.hmm GCF_024721975.1_ASM2472197v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:04,576] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:04,578] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbd009f62-ffb0-4b6e-8b58-9623eb5778fa/GCF_024721975.1_ASM2472197v1_genomic.fna.gz]
[2024-01-24 12:41:04,626] [INFO] Query marker FASTA was written to GCF_024721975.1_ASM2472197v1_genomic.fna/markers.fasta
[2024-01-24 12:41:04,627] [INFO] Task started: Blastn
[2024-01-24 12:41:04,627] [INFO] Running command: blastn -query GCF_024721975.1_ASM2472197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference/reference_markers.fasta -out GCF_024721975.1_ASM2472197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:05,271] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:05,275] [INFO] Selected 29 target genomes.
[2024-01-24 12:41:05,275] [INFO] Target genome list was writen to GCF_024721975.1_ASM2472197v1_genomic.fna/target_genomes.txt
[2024-01-24 12:41:05,285] [INFO] Task started: fastANI
[2024-01-24 12:41:05,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd009f62-ffb0-4b6e-8b58-9623eb5778fa/GCF_024721975.1_ASM2472197v1_genomic.fna.gz --refList GCF_024721975.1_ASM2472197v1_genomic.fna/target_genomes.txt --output GCF_024721975.1_ASM2472197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:27,067] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:27,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:27,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:27,092] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:41:27,092] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:41:27,092] [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 macquariensis subsp. macquariensis	strain=DSM 2	GCA_001637165.1	1468	948756	type	True	78.0555	128	1959	95	below_threshold
Paenibacillus macquariensis	strain=ATCC 23464	GCA_900156375.1	948756	948756	type	True	78.0049	127	1959	95	below_threshold
Paenibacillus antarcticus	strain=CECT 5836	GCA_001637225.1	253703	253703	type	True	77.9409	104	1959	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	77.3988	74	1959	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	77.2992	57	1959	95	below_threshold
Paenibacillus albiflavus	strain=18JY21-1	GCA_004344915.1	2545760	2545760	type	True	77.2588	65	1959	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.0646	69	1959	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	77.0365	87	1959	95	below_threshold
Paenibacillus xylanexedens	strain=DSM 21292	GCA_017874615.1	528191	528191	suspected-type	True	76.7122	65	1959	95	below_threshold
Paenibacillus turicensis	strain=DSM 14349	GCA_017873435.1	160487	160487	type	True	76.578	60	1959	95	below_threshold
Paenibacillus pectinilyticus	strain=KCTC13222	GCA_001700435.1	512399	512399	type	True	76.5414	64	1959	95	below_threshold
Paenibacillus assamensis	strain=DSM 18201	GCA_000422445.1	311244	311244	type	True	76.532	62	1959	95	below_threshold
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	76.154	56	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:27,095] [INFO] DFAST Taxonomy check result was written to GCF_024721975.1_ASM2472197v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:27,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:27,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:27,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference/checkm_data
[2024-01-24 12:41:27,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:27,158] [INFO] Task started: CheckM
[2024-01-24 12:41:27,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721975.1_ASM2472197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721975.1_ASM2472197v1_genomic.fna/checkm_input GCF_024721975.1_ASM2472197v1_genomic.fna/checkm_result
[2024-01-24 12:42:07,276] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:07,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:07,301] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:07,302] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:07,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721975.1_ASM2472197v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:07,303] [INFO] Task started: Blastn
[2024-01-24 12:42:07,303] [INFO] Running command: blastn -query GCF_024721975.1_ASM2472197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b6b665-5550-47db-9313-75b25aaf3359/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721975.1_ASM2472197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:08,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:08,176] [INFO] Selected 21 target genomes.
[2024-01-24 12:42:08,176] [INFO] Target genome list was writen to GCF_024721975.1_ASM2472197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:08,229] [INFO] Task started: fastANI
[2024-01-24 12:42:08,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd009f62-ffb0-4b6e-8b58-9623eb5778fa/GCF_024721975.1_ASM2472197v1_genomic.fna.gz --refList GCF_024721975.1_ASM2472197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721975.1_ASM2472197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:29,446] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:29,462] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:42:29,462] [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_019113605.1	s__Paenibacillus_C intestinavium	84.1263	811	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637225.1	s__Paenibacillus antarcticus	77.9752	103	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156375.1	s__Paenibacillus macquariensis	77.9514	129	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.68	95.38	0.90	0.81	3	-
GCF_018403185.1	s__Paenibacillus_C montaniterrae	77.9281	259	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956095.1	s__Paenibacillus_C sp001956095	77.833	139	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280845.1	s__Paenibacillus_C sp001280845	77.8141	133	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217535.1	s__Paenibacillus_C sp003217535	77.2583	82	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337375.1	s__Paenibacillus_C prosopidis	77.0365	87	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570725.1	s__Paenibacillus amylolyticus_A	76.7026	56	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.59	97.52	0.92	0.91	3	-
GCF_003268635.1	s__Paenibacillus sp003268635	76.6982	61	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614975.1	s__Paenibacillus polymyxa_E	76.6288	63	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873435.1	s__Paenibacillus_A turicensis	76.5823	61	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422445.1	s__Paenibacillus_B assamensis	76.5574	62	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428045.1	s__Paenibacillus_E sp001428045	76.4936	59	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908805.1	s__Paenibacillus_J nicotianae	76.4489	77	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653565.1	s__Paenibacillus_E oryzisoli	76.154	56	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912005.1	s__Paenibacillus sp012912005	76.0575	64	1959	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:29,465] [INFO] GTDB search result was written to GCF_024721975.1_ASM2472197v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:29,466] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:29,469] [INFO] DFAST_QC result json was written to GCF_024721975.1_ASM2472197v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:29,470] [INFO] DFAST_QC completed!
[2024-01-24 12:42:29,470] [INFO] Total running time: 0h1m38s