[2024-01-24 13:57:41,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference
[2024-01-24 13:57:42,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:42,905] [INFO] Task started: Prodigal
[2024-01-24 13:57:42,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg876845f3-96f4-4739-890e-7bde89a99dea/GCF_005938385.1_ASM593838v1_genomic.fna.gz | prodigal -d GCF_005938385.1_ASM593838v1_genomic.fna/cds.fna -a GCF_005938385.1_ASM593838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:09,732] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:09,733] [INFO] Task started: HMMsearch
[2024-01-24 13:58:09,733] [INFO] Running command: hmmsearch --tblout GCF_005938385.1_ASM593838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference/reference_markers.hmm GCF_005938385.1_ASM593838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:10,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:10,219] [INFO] Found 6/6 markers.
[2024-01-24 13:58:10,302] [INFO] Query marker FASTA was written to GCF_005938385.1_ASM593838v1_genomic.fna/markers.fasta
[2024-01-24 13:58:10,303] [INFO] Task started: Blastn
[2024-01-24 13:58:10,303] [INFO] Running command: blastn -query GCF_005938385.1_ASM593838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference/reference_markers.fasta -out GCF_005938385.1_ASM593838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:10,993] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:10,996] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:10,997] [INFO] Target genome list was writen to GCF_005938385.1_ASM593838v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:11,006] [INFO] Task started: fastANI
[2024-01-24 13:58:11,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg876845f3-96f4-4739-890e-7bde89a99dea/GCF_005938385.1_ASM593838v1_genomic.fna.gz --refList GCF_005938385.1_ASM593838v1_genomic.fna/target_genomes.txt --output GCF_005938385.1_ASM593838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:34,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:34,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:34,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:34,632] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:34,633] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:34,633] [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 mesophilus	strain=SYSU K30004	GCA_005938385.1	2582849	2582849	type	True	100.0	2876	2881	95	conclusive
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	84.0001	1777	2881	95	below_threshold
Paenibacillus ginsengarvi	strain=KCTC 13059	GCA_003626695.1	400777	400777	type	True	80.545	1233	2881	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	80.1625	925	2881	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	79.572	967	2881	95	below_threshold
Paenibacillus allorhizosphaerae	strain=CIP 111802	GCA_910594985.1	2849866	2849866	type	True	77.8784	342	2881	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	77.0856	221	2881	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.9722	286	2881	95	below_threshold
Paenibacillus tianmuensis	strain=CGMCC 1.8946	GCA_900100345.1	624147	624147	type	True	76.9178	228	2881	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.879	256	2881	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	76.8512	189	2881	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	76.7699	367	2881	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.6163	173	2881	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.4645	121	2881	95	below_threshold
Paenibacillus oryzisoli	strain=1ZS3-15	GCA_001653565.1	1850517	1850517	type	True	76.3538	57	2881	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:34,635] [INFO] DFAST Taxonomy check result was written to GCF_005938385.1_ASM593838v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:34,635] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:34,635] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:34,636] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference/checkm_data
[2024-01-24 13:58:34,637] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:34,720] [INFO] Task started: CheckM
[2024-01-24 13:58:34,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005938385.1_ASM593838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005938385.1_ASM593838v1_genomic.fna/checkm_input GCF_005938385.1_ASM593838v1_genomic.fna/checkm_result
[2024-01-24 13:59:44,900] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:44,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:44,929] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:44,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:44,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005938385.1_ASM593838v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:44,930] [INFO] Task started: Blastn
[2024-01-24 13:59:44,930] [INFO] Running command: blastn -query GCF_005938385.1_ASM593838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05a6ca92-2805-4136-b067-1da89e928f42/dqc_reference/reference_markers_gtdb.fasta -out GCF_005938385.1_ASM593838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:45,742] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:45,746] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:45,746] [INFO] Target genome list was writen to GCF_005938385.1_ASM593838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:45,771] [INFO] Task started: fastANI
[2024-01-24 13:59:45,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg876845f3-96f4-4739-890e-7bde89a99dea/GCF_005938385.1_ASM593838v1_genomic.fna.gz --refList GCF_005938385.1_ASM593838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005938385.1_ASM593838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:03,623] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:03,637] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:03,637] [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_005938385.1	s__Paenibacillus_AB mesophilus	100.0	2876	2881	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	conclusive
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	84.0089	1775	2881	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_003626695.1	s__Paenibacillus_AB ginsengarvi	80.5581	1228	2881	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_003217775.1	s__Paenibacillus_AB flagellatus	80.1775	923	2881	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_014705615.1	s__Paenibacillus_AB sp014705615	79.5586	969	2881	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_910593845.1	s__Paenibacillus_G solanacearum	77.5259	341	2881	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_014212175.1	s__Cohnella xylanilytica	77.0553	222	2881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_004514475.1	s__MEC069 sp004514475	76.9514	196	2881	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_018403265.1	s__J31TS4 sp018403265	76.883	220	2881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__J31TS4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	76.8124	192	2881	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_009363095.1	s__Paenibacillus cellulositrophicus_A	76.7929	146	2881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.73	96.59	0.92	0.91	14	-
GCF_001653565.1	s__Paenibacillus_E oryzisoli	76.3291	58	2881	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:03,639] [INFO] GTDB search result was written to GCF_005938385.1_ASM593838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:03,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:03,644] [INFO] DFAST_QC result json was written to GCF_005938385.1_ASM593838v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:03,644] [INFO] DFAST_QC completed!
[2024-01-24 14:00:03,644] [INFO] Total running time: 0h2m22s