[2024-01-24 14:38:59,911] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:59,913] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:59,913] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference
[2024-01-24 14:39:01,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:01,191] [INFO] Task started: Prodigal
[2024-01-24 14:39:01,191] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc8b6f28-dc62-4cfb-acd5-bf270e0b0713/GCF_005869875.1_ASM586987v1_genomic.fna.gz | prodigal -d GCF_005869875.1_ASM586987v1_genomic.fna/cds.fna -a GCF_005869875.1_ASM586987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:19,354] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:19,354] [INFO] Task started: HMMsearch
[2024-01-24 14:39:19,355] [INFO] Running command: hmmsearch --tblout GCF_005869875.1_ASM586987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference/reference_markers.hmm GCF_005869875.1_ASM586987v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:19,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:19,667] [INFO] Found 6/6 markers.
[2024-01-24 14:39:19,708] [INFO] Query marker FASTA was written to GCF_005869875.1_ASM586987v1_genomic.fna/markers.fasta
[2024-01-24 14:39:19,708] [INFO] Task started: Blastn
[2024-01-24 14:39:19,709] [INFO] Running command: blastn -query GCF_005869875.1_ASM586987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference/reference_markers.fasta -out GCF_005869875.1_ASM586987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:20,393] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:20,396] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:20,397] [INFO] Target genome list was writen to GCF_005869875.1_ASM586987v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:20,406] [INFO] Task started: fastANI
[2024-01-24 14:39:20,407] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc8b6f28-dc62-4cfb-acd5-bf270e0b0713/GCF_005869875.1_ASM586987v1_genomic.fna.gz --refList GCF_005869875.1_ASM586987v1_genomic.fna/target_genomes.txt --output GCF_005869875.1_ASM586987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:35,392] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:35,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:35,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:35,408] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:35,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:35,409] [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 pinistramenti	strain=ASL46	GCA_005869875.1	1768003	1768003	type	True	100.0	1379	1379	95	conclusive
Paenibacillus physcomitrellae	strain=CGMCC 1.15044	GCA_014640575.1	1619311	1619311	type	True	81.0194	715	1379	95	below_threshold
Paenibacillus physcomitrellae	strain=XB	GCA_002240225.1	1619311	1619311	type	True	80.9849	746	1379	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	80.7339	745	1379	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	78.7953	420	1379	95	below_threshold
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	77.5575	133	1379	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.5521	244	1379	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.4946	163	1379	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.2974	160	1379	95	below_threshold
Paenibacillus lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	77.2821	131	1379	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	77.1362	113	1379	95	below_threshold
Paenibacillus donghaensis	strain=KCTC 13049	GCA_002192415.1	414771	414771	type	True	77.1223	193	1379	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.7517	196	1379	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	76.4699	128	1379	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	76.4232	90	1379	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.259	103	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:35,411] [INFO] DFAST Taxonomy check result was written to GCF_005869875.1_ASM586987v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:35,411] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:35,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:35,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference/checkm_data
[2024-01-24 14:39:35,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:35,459] [INFO] Task started: CheckM
[2024-01-24 14:39:35,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005869875.1_ASM586987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005869875.1_ASM586987v1_genomic.fna/checkm_input GCF_005869875.1_ASM586987v1_genomic.fna/checkm_result
[2024-01-24 14:40:12,892] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:12,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:12,913] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:12,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:12,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005869875.1_ASM586987v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:12,914] [INFO] Task started: Blastn
[2024-01-24 14:40:12,914] [INFO] Running command: blastn -query GCF_005869875.1_ASM586987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1f2c894-f611-4d22-bc75-b160a21382c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_005869875.1_ASM586987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:13,762] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:13,766] [INFO] Selected 17 target genomes.
[2024-01-24 14:40:13,766] [INFO] Target genome list was writen to GCF_005869875.1_ASM586987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:13,783] [INFO] Task started: fastANI
[2024-01-24 14:40:13,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc8b6f28-dc62-4cfb-acd5-bf270e0b0713/GCF_005869875.1_ASM586987v1_genomic.fna.gz --refList GCF_005869875.1_ASM586987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005869875.1_ASM586987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:30,880] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:30,895] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:30,895] [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_005869875.1	s__Paenibacillus_A pinistramenti	100.0	1379	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002240225.1	s__Paenibacillus_A physcomitrellae	80.9849	746	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001685395.1	s__Paenibacillus_A yonginensis	80.7417	745	1379	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_900021165.1	s__Paenibacillus_A phocaensis	77.7304	232	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	77.4669	152	1379	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_003614185.1	s__Paenibacillus_A aceti	77.4496	163	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018403325.1	s__Paenibacillus_A vini	77.3117	232	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	77.2964	206	1379	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_000159955.1	s__Paenibacillus_A sp000159955	77.2765	233	1379	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_001486585.1	s__Paenibacillus_A senegalimassiliensis	77.2469	145	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002257645.1	s__Paenibacillus sp002257645	77.229	221	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987955.1	s__Paenibacillus sp000987955	77.2234	170	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931855.1	s__Paenibacillus_A lentus	77.2105	133	1379	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_900099765.1	s__Paenibacillus typhae	77.2076	218	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
GCF_000758625.1	s__Paenibacillus sp000758625	77.1787	222	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002192415.1	s__Paenibacillus donghaensis	77.1223	193	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002189105.1	s__Saccharibacillus sp002189105	76.9264	135	1379	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:30,899] [INFO] GTDB search result was written to GCF_005869875.1_ASM586987v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:30,899] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:30,904] [INFO] DFAST_QC result json was written to GCF_005869875.1_ASM586987v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:30,905] [INFO] DFAST_QC completed!
[2024-01-24 14:40:30,905] [INFO] Total running time: 0h1m31s