[2024-01-25 18:11:35,827] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference
[2024-01-25 18:11:36,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,928] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,928] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4ef2b31-1a64-4482-a990-0f33b15ee74a/GCF_018403685.1_ASM1840368v1_genomic.fna.gz | prodigal -d GCF_018403685.1_ASM1840368v1_genomic.fna/cds.fna -a GCF_018403685.1_ASM1840368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:49,225] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:49,225] [INFO] Task started: HMMsearch
[2024-01-25 18:11:49,225] [INFO] Running command: hmmsearch --tblout GCF_018403685.1_ASM1840368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference/reference_markers.hmm GCF_018403685.1_ASM1840368v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:49,511] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:49,513] [INFO] Found 6/6 markers.
[2024-01-25 18:11:49,559] [INFO] Query marker FASTA was written to GCF_018403685.1_ASM1840368v1_genomic.fna/markers.fasta
[2024-01-25 18:11:49,560] [INFO] Task started: Blastn
[2024-01-25 18:11:49,560] [INFO] Running command: blastn -query GCF_018403685.1_ASM1840368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference/reference_markers.fasta -out GCF_018403685.1_ASM1840368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:50,155] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:50,157] [INFO] Selected 29 target genomes.
[2024-01-25 18:11:50,158] [INFO] Target genome list was writen to GCF_018403685.1_ASM1840368v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:50,211] [INFO] Task started: fastANI
[2024-01-25 18:11:50,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4ef2b31-1a64-4482-a990-0f33b15ee74a/GCF_018403685.1_ASM1840368v1_genomic.fna.gz --refList GCF_018403685.1_ASM1840368v1_genomic.fna/target_genomes.txt --output GCF_018403685.1_ASM1840368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:20,547] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:20,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:20,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:20,562] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:20,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:20,562] [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
Xylanibacillus composti	strain=K13	GCA_018403685.1	1572762	1572762	type	True	100.0	1487	1492	95	conclusive
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	78.0381	94	1492	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.7656	105	1492	95	below_threshold
Paenibacillus turpanensis	strain=YIM B00363	GCA_011421635.1	2689078	2689078	type	True	76.3972	74	1492	95	below_threshold
Paenibacillus elgii	strain=NBRC 100335	GCA_004000865.1	189691	189691	type	True	76.3861	97	1492	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.3705	57	1492	95	below_threshold
Paenibacillus contaminans	strain=CKOBP-6	GCA_003285015.1	450362	450362	type	True	76.3094	95	1492	95	below_threshold
Paenibacillus koleovorans	strain=NBRC 103111	GCA_004000845.1	121608	121608	type	True	76.2517	73	1492	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	76.1493	74	1492	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	76.1043	110	1492	95	below_threshold
Paenibacillus nanensis	strain=DSM 22867	GCA_003583765.1	393251	393251	type	True	76.0712	92	1492	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	76.0624	89	1492	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.054	78	1492	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	75.9981	99	1492	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	75.9685	57	1492	95	below_threshold
Paenibacillus athensensis	strain=MEC069	GCA_004514475.2	1967502	1967502	type	True	75.9615	94	1492	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	75.9605	59	1492	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	75.8458	85	1492	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	75.7452	61	1492	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	75.7227	110	1492	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	75.7213	74	1492	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	75.7059	50	1492	95	below_threshold
Paenibacillus pinistramenti	strain=ASL46	GCA_005869875.1	1768003	1768003	type	True	75.5143	58	1492	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:20,564] [INFO] DFAST Taxonomy check result was written to GCF_018403685.1_ASM1840368v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:20,564] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:20,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:20,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference/checkm_data
[2024-01-25 18:12:20,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:20,612] [INFO] Task started: CheckM
[2024-01-25 18:12:20,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018403685.1_ASM1840368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018403685.1_ASM1840368v1_genomic.fna/checkm_input GCF_018403685.1_ASM1840368v1_genomic.fna/checkm_result
[2024-01-25 18:12:58,839] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:58,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:58,858] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:58,858] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:58,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018403685.1_ASM1840368v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:58,859] [INFO] Task started: Blastn
[2024-01-25 18:12:58,859] [INFO] Running command: blastn -query GCF_018403685.1_ASM1840368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg215c6113-c3bc-4878-b1b6-c85527ecf96f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018403685.1_ASM1840368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:59,685] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:59,689] [INFO] Selected 28 target genomes.
[2024-01-25 18:12:59,689] [INFO] Target genome list was writen to GCF_018403685.1_ASM1840368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:59,703] [INFO] Task started: fastANI
[2024-01-25 18:12:59,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4ef2b31-1a64-4482-a990-0f33b15ee74a/GCF_018403685.1_ASM1840368v1_genomic.fna.gz --refList GCF_018403685.1_ASM1840368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018403685.1_ASM1840368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:28,074] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:28,090] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:28,090] [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_018403685.1	s__Xylanibacillus composti	100.0	1487	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__K13;g__Xylanibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018918005.1	s__MSJ-34 sp018918005	80.4791	90	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403665.1	s__Paenibacillus_AH cisolokensis	77.9626	96	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_AH	95.0	98.86	98.86	0.88	0.88	2	-
GCF_000380965.1	s__Paenibacillus_M ginsengihumi	76.7656	105	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015472005.1	s__DA-C8 sp015472005	76.686	58	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__DA-C8;g__DA-C8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159955.1	s__Paenibacillus_A sp000159955	76.5603	60	1492	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_011421635.1	s__Paenibacillus_AK turpanensis	76.3972	74	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__YIM-B00363;g__Paenibacillus_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399685.1	s__Paenibacillus_G sp001399685	76.3445	96	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285015.1	s__Paenibacillus_V contaminans	76.3094	95	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_V	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101595.1	s__Paenibacillus_G sp900101595	76.2153	101	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003626695.1	s__Paenibacillus_AB ginsengarvi	76.1831	81	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002243345.2	s__Paenibacillus_O sp002243345	76.1684	96	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.98	99.98	0.98	0.98	4	-
GCF_003605435.1	s__Paenibacillus_C pinisoli	76.1493	74	1492	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_003591485.1	s__Paenibacillus_C sp003591485	76.1021	66	1492	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_003583765.1	s__Paenibacillus_C nanensis	76.0712	92	1492	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_014212175.1	s__Cohnella xylanilytica	76.0624	89	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_907165215.1	s__Thermobacillus xylanilyticus	76.054	78	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_003388735.1	s__Paenibacillus_C paeoniae	75.9685	57	1492	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_004514475.1	s__MEC069 sp004514475	75.9652	94	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__MEC069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001675.1	s__Cohnella sp003001675	75.893	81	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004354045.1	s__Paenibacillus_S piri	75.8512	73	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520735.1	s__Paenibacillus forsythiae	75.771	58	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004764705.1	s__R196 sp004764705	75.7227	110	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__R196	95.0	95.77	95.77	0.86	0.86	2	-
GCF_900021165.1	s__Paenibacillus_A phocaensis	75.7213	74	1492	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_015326965.1	s__Paenibacillus sp001860525	75.5843	53	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.48	95.93	0.88	0.85	4	-
GCF_005869875.1	s__Paenibacillus_A pinistramenti	75.5143	58	1492	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:28,091] [INFO] GTDB search result was written to GCF_018403685.1_ASM1840368v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:28,092] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:28,096] [INFO] DFAST_QC result json was written to GCF_018403685.1_ASM1840368v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:28,096] [INFO] DFAST_QC completed!
[2024-01-25 18:13:28,096] [INFO] Total running time: 0h1m52s