[2024-01-24 13:49:29,444] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,447] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,447] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference
[2024-01-24 13:49:30,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,816] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,816] [INFO] Running command: gunzip -c /var/lib/cwl/stge07f939b-59fe-46f6-bec1-30995c3f1a2a/GCF_007066085.1_ASM706608v1_genomic.fna.gz | prodigal -d GCF_007066085.1_ASM706608v1_genomic.fna/cds.fna -a GCF_007066085.1_ASM706608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:53,740] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:53,740] [INFO] Task started: HMMsearch
[2024-01-24 13:49:53,740] [INFO] Running command: hmmsearch --tblout GCF_007066085.1_ASM706608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference/reference_markers.hmm GCF_007066085.1_ASM706608v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:54,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:54,203] [INFO] Found 6/6 markers.
[2024-01-24 13:49:54,255] [INFO] Query marker FASTA was written to GCF_007066085.1_ASM706608v1_genomic.fna/markers.fasta
[2024-01-24 13:49:54,256] [INFO] Task started: Blastn
[2024-01-24 13:49:54,256] [INFO] Running command: blastn -query GCF_007066085.1_ASM706608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference/reference_markers.fasta -out GCF_007066085.1_ASM706608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:54,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:54,927] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:54,928] [INFO] Target genome list was writen to GCF_007066085.1_ASM706608v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:54,944] [INFO] Task started: fastANI
[2024-01-24 13:49:54,945] [INFO] Running command: fastANI --query /var/lib/cwl/stge07f939b-59fe-46f6-bec1-30995c3f1a2a/GCF_007066085.1_ASM706608v1_genomic.fna.gz --refList GCF_007066085.1_ASM706608v1_genomic.fna/target_genomes.txt --output GCF_007066085.1_ASM706608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:12,008] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:12,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:12,021] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:50:12,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:12,022] [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 thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	100.0	2204	2204	95	conclusive
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	99.9776	2156	2204	95	conclusive
Paenibacillus thiaminolyticus	strain=NBRC 15656	GCA_004001005.1	49283	49283	type	True	99.9108	2048	2204	95	conclusive
Paenibacillus popilliae	strain=ATCC 14706	GCA_000315235.1	78057	78057	type	True	88.7333	879	2204	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	78.2277	117	2204	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.4192	208	2204	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.0151	157	2204	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.9616	109	2204	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.7365	165	2204	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.5713	99	2204	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	76.5287	136	2204	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	76.4721	190	2204	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	76.3183	102	2204	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.2773	148	2204	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.2043	113	2204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,023] [INFO] DFAST Taxonomy check result was written to GCF_007066085.1_ASM706608v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:12,024] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:12,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:12,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference/checkm_data
[2024-01-24 13:50:12,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:12,091] [INFO] Task started: CheckM
[2024-01-24 13:50:12,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007066085.1_ASM706608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007066085.1_ASM706608v1_genomic.fna/checkm_input GCF_007066085.1_ASM706608v1_genomic.fna/checkm_result
[2024-01-24 13:51:14,511] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:14,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:14,535] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:14,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:14,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007066085.1_ASM706608v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:14,536] [INFO] Task started: Blastn
[2024-01-24 13:51:14,536] [INFO] Running command: blastn -query GCF_007066085.1_ASM706608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd2f375c-83ba-4ac2-8460-a42ecbfd2687/dqc_reference/reference_markers_gtdb.fasta -out GCF_007066085.1_ASM706608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:15,327] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:15,332] [INFO] Selected 6 target genomes.
[2024-01-24 13:51:15,332] [INFO] Target genome list was writen to GCF_007066085.1_ASM706608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:15,345] [INFO] Task started: fastANI
[2024-01-24 13:51:15,345] [INFO] Running command: fastANI --query /var/lib/cwl/stge07f939b-59fe-46f6-bec1-30995c3f1a2a/GCF_007066085.1_ASM706608v1_genomic.fna.gz --refList GCF_007066085.1_ASM706608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007066085.1_ASM706608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:25,890] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:25,902] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:25,902] [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_007066085.1	s__Paenibacillus_B thiaminolyticus	100.0	2204	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.67	95.07	0.96	0.85	7	conclusive
GCF_000245555.1	s__Paenibacillus_B dendritiformis_A	92.7531	1739	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.57	96.94	0.92	0.90	3	-
GCF_018403065.1	s__Paenibacillus_B dendritiformis_B	91.274	1610	2204	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_015845845.1	s__Paenibacillus_B dendritiformis_C	91.0907	1619	2204	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_013266915.1	s__Paenibacillus_B sp900539405	90.6102	1692	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	99.54	99.32	0.96	0.95	4	-
GCF_000315235.1	s__Paenibacillus_B popilliae	88.7333	879	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:25,904] [INFO] GTDB search result was written to GCF_007066085.1_ASM706608v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:25,904] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:25,907] [INFO] DFAST_QC result json was written to GCF_007066085.1_ASM706608v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:25,907] [INFO] DFAST_QC completed!
[2024-01-24 13:51:25,908] [INFO] Total running time: 0h1m56s