[2024-01-24 12:40:20,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,895] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,895] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference
[2024-01-24 12:40:22,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:22,118] [INFO] Task started: Prodigal
[2024-01-24 12:40:22,119] [INFO] Running command: gunzip -c /var/lib/cwl/stg417f2fd6-8c7b-4522-a168-3fce109d1a5b/GCF_018919145.1_ASM1891914v1_genomic.fna.gz | prodigal -d GCF_018919145.1_ASM1891914v1_genomic.fna/cds.fna -a GCF_018919145.1_ASM1891914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:35,597] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:35,598] [INFO] Task started: HMMsearch
[2024-01-24 12:40:35,598] [INFO] Running command: hmmsearch --tblout GCF_018919145.1_ASM1891914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference/reference_markers.hmm GCF_018919145.1_ASM1891914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:35,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:35,895] [INFO] Found 6/6 markers.
[2024-01-24 12:40:35,935] [INFO] Query marker FASTA was written to GCF_018919145.1_ASM1891914v1_genomic.fna/markers.fasta
[2024-01-24 12:40:35,936] [INFO] Task started: Blastn
[2024-01-24 12:40:35,936] [INFO] Running command: blastn -query GCF_018919145.1_ASM1891914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference/reference_markers.fasta -out GCF_018919145.1_ASM1891914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:36,532] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:36,535] [INFO] Selected 19 target genomes.
[2024-01-24 12:40:36,536] [INFO] Target genome list was writen to GCF_018919145.1_ASM1891914v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:36,544] [INFO] Task started: fastANI
[2024-01-24 12:40:36,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg417f2fd6-8c7b-4522-a168-3fce109d1a5b/GCF_018919145.1_ASM1891914v1_genomic.fna.gz --refList GCF_018919145.1_ASM1891914v1_genomic.fna/target_genomes.txt --output GCF_018919145.1_ASM1891914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:54,374] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:54,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:54,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:54,395] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:54,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:54,396] [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 brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	100.0	1716	1720	95	conclusive
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	92.2782	1400	1720	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	78.4651	353	1720	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.9924	305	1720	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.9547	271	1720	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	77.8442	322	1720	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.763	231	1720	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.7577	262	1720	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.6925	258	1720	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.6661	319	1720	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	77.6638	305	1720	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	77.6486	326	1720	95	below_threshold
Paenibacillus lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	77.5815	210	1720	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	77.5726	231	1720	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.3862	191	1720	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.1407	124	1720	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	76.9733	175	1720	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	76.7847	116	1720	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	76.6752	93	1720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:54,397] [INFO] DFAST Taxonomy check result was written to GCF_018919145.1_ASM1891914v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:54,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:54,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:54,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference/checkm_data
[2024-01-24 12:40:54,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:54,446] [INFO] Task started: CheckM
[2024-01-24 12:40:54,446] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018919145.1_ASM1891914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018919145.1_ASM1891914v1_genomic.fna/checkm_input GCF_018919145.1_ASM1891914v1_genomic.fna/checkm_result
[2024-01-24 12:41:37,889] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:37,891] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:37,911] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:37,911] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:37,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018919145.1_ASM1891914v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:37,912] [INFO] Task started: Blastn
[2024-01-24 12:41:37,913] [INFO] Running command: blastn -query GCF_018919145.1_ASM1891914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8e122d-9175-4508-b8dd-d4e0818c0c89/dqc_reference/reference_markers_gtdb.fasta -out GCF_018919145.1_ASM1891914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:38,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:38,694] [INFO] Selected 20 target genomes.
[2024-01-24 12:41:38,694] [INFO] Target genome list was writen to GCF_018919145.1_ASM1891914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:38,709] [INFO] Task started: fastANI
[2024-01-24 12:41:38,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg417f2fd6-8c7b-4522-a168-3fce109d1a5b/GCF_018919145.1_ASM1891914v1_genomic.fna.gz --refList GCF_018919145.1_ASM1891914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018919145.1_ASM1891914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:57,403] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:57,428] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:57,428] [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_018919145.1	s__Paenibacillus_A sp018919145	100.0	1716	1720	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_000455265.1	s__Paenibacillus_A antibioticophila	92.2782	1400	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.82	95.80	0.91	0.82	4	-
GCF_003337355.1	s__Paenibacillus_A phaseoli	79.1712	433	1720	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_018403325.1	s__Paenibacillus_A vini	79.0751	440	1720	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_002439285.1	s__Paenibacillus_A sp002439285	78.6216	335	1720	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_008084145.1	s__Paenibacillus_A faecis	78.2831	368	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	-
GCF_003614185.1	s__Paenibacillus_A aceti	77.9564	269	1720	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_000159955.1	s__Paenibacillus_A sp000159955	77.8488	285	1720	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_001486505.1	s__Paenibacillus_A rubinfantis	77.8372	321	1720	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_900069005.2	s__Paenibacillus_A sp900069005	77.7035	269	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.72	99.44	0.97	0.94	3	-
GCF_001403875.1	s__Paenibacillus_A ihumii	77.69	257	1720	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_004000745.1	s__Paenibacillus_A barengoltzii	77.6564	281	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.39	97.66	0.91	0.90	5	-
GCF_900454495.1	s__Paenibacillus_A macerans	77.652	325	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCF_009725165.1	s__Paenibacillus_A woosongensis	77.4646	239	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	95.99	95.99	0.91	0.91	2	-
GCF_005577435.1	s__Paenibacillus sp005577435	77.1424	123	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.84	98.84	0.91	0.91	2	-
GCF_004001045.1	s__Paenibacillus chibensis	76.9742	174	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001373415.1	s__Paenibacillus dakarensis	76.7666	115	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272015.1	s__Paenibacillus campinasensis	76.6908	177	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_018403065.1	s__Paenibacillus_B dendritiformis_B	76.2608	101	1720	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_005765165.1	s__Paenibacillus_AE antri	76.0701	50	1720	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:57,430] [INFO] GTDB search result was written to GCF_018919145.1_ASM1891914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:57,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:57,434] [INFO] DFAST_QC result json was written to GCF_018919145.1_ASM1891914v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:57,435] [INFO] DFAST_QC completed!
[2024-01-24 12:41:57,435] [INFO] Total running time: 0h1m37s