[2024-01-24 10:58:06,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,475] [INFO] DQC Reference Directory: /var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference
[2024-01-24 10:58:09,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,635] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc5b1e31-93ab-4ea8-af76-9ad53d7a7807/GCF_002240225.1_ASM224022v1_genomic.fna.gz | prodigal -d GCF_002240225.1_ASM224022v1_genomic.fna/cds.fna -a GCF_002240225.1_ASM224022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:22,144] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:22,145] [INFO] Task started: HMMsearch
[2024-01-24 10:58:22,145] [INFO] Running command: hmmsearch --tblout GCF_002240225.1_ASM224022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference/reference_markers.hmm GCF_002240225.1_ASM224022v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:22,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:22,507] [INFO] Found 6/6 markers.
[2024-01-24 10:58:22,553] [INFO] Query marker FASTA was written to GCF_002240225.1_ASM224022v1_genomic.fna/markers.fasta
[2024-01-24 10:58:22,553] [INFO] Task started: Blastn
[2024-01-24 10:58:22,553] [INFO] Running command: blastn -query GCF_002240225.1_ASM224022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference/reference_markers.fasta -out GCF_002240225.1_ASM224022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:23,146] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:23,151] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:23,151] [INFO] Target genome list was writen to GCF_002240225.1_ASM224022v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:23,159] [INFO] Task started: fastANI
[2024-01-24 10:58:23,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc5b1e31-93ab-4ea8-af76-9ad53d7a7807/GCF_002240225.1_ASM224022v1_genomic.fna.gz --refList GCF_002240225.1_ASM224022v1_genomic.fna/target_genomes.txt --output GCF_002240225.1_ASM224022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:35,572] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:35,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:35,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:35,587] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:35,588] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:35,588] [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 physcomitrellae	strain=XB	GCA_002240225.1	1619311	1619311	type	True	100.0	1609	1609	95	conclusive
Paenibacillus physcomitrellae	strain=CGMCC 1.15044	GCA_014640575.1	1619311	1619311	type	True	99.9836	1571	1609	95	conclusive
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	89.3738	1326	1609	95	below_threshold
Paenibacillus pinistramenti	strain=ASL46	GCA_005869875.1	1768003	1768003	type	True	80.8277	745	1609	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	78.9862	457	1609	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	77.6585	180	1609	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.5652	180	1609	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.4502	283	1609	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	77.3801	179	1609	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.3798	166	1609	95	below_threshold
Paenibacillus massiliensis	strain=DSM 16942	GCA_000377505.1	225917	225917	type	True	77.3471	109	1609	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	76.948	110	1609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:35,589] [INFO] DFAST Taxonomy check result was written to GCF_002240225.1_ASM224022v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:35,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:35,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:35,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference/checkm_data
[2024-01-24 10:58:35,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:35,637] [INFO] Task started: CheckM
[2024-01-24 10:58:35,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002240225.1_ASM224022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002240225.1_ASM224022v1_genomic.fna/checkm_input GCF_002240225.1_ASM224022v1_genomic.fna/checkm_result
[2024-01-24 10:59:16,747] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:16,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:16,771] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:16,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:16,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002240225.1_ASM224022v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:16,772] [INFO] Task started: Blastn
[2024-01-24 10:59:16,773] [INFO] Running command: blastn -query GCF_002240225.1_ASM224022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga92665e5-f739-4a1d-835c-dc01693305a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002240225.1_ASM224022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:17,612] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:17,617] [INFO] Selected 15 target genomes.
[2024-01-24 10:59:17,617] [INFO] Target genome list was writen to GCF_002240225.1_ASM224022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:17,645] [INFO] Task started: fastANI
[2024-01-24 10:59:17,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc5b1e31-93ab-4ea8-af76-9ad53d7a7807/GCF_002240225.1_ASM224022v1_genomic.fna.gz --refList GCF_002240225.1_ASM224022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002240225.1_ASM224022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:34,310] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:34,327] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:34,328] [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_002240225.1	s__Paenibacillus_A physcomitrellae	100.0	1609	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001685395.1	s__Paenibacillus_A yonginensis	89.3802	1329	1609	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_005869875.1	s__Paenibacillus_A pinistramenti	80.8318	746	1609	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_003060825.1	s__Paenibacillus_A sp003060825	78.9956	252	1609	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_000756615.1	s__Paenibacillus durus	78.7745	158	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863545.1	s__Paenibacillus lautus_A	77.9617	190	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.37	95.82	0.93	0.90	10	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	77.8596	254	1609	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_900086655.1	s__Paenibacillus_A tuaregi	77.6768	222	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.53	97.06	0.96	0.92	3	-
GCF_003863965.1	s__Paenibacillus_A oralis	77.6533	294	1609	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_003994465.1	s__Paenibacillus_A zeisoli	77.6456	182	1609	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	77.4751	246	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002189105.1	s__Saccharibacillus sp002189105	76.9908	136	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386535.1	s__Paenibacillus_Z taihuensis	76.9015	110	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204885.1	s__Paenibacillus tritici	76.8744	179	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
GCF_012935325.2	s__Paenibacillus_C sp012935325	76.4675	78	1609	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:34,331] [INFO] GTDB search result was written to GCF_002240225.1_ASM224022v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:34,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:34,338] [INFO] DFAST_QC result json was written to GCF_002240225.1_ASM224022v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:34,338] [INFO] DFAST_QC completed!
[2024-01-24 10:59:34,338] [INFO] Total running time: 0h1m28s