[2024-01-24 13:56:27,409] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,411] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,411] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference
[2024-01-24 13:56:28,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,640] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg36a05de3-a430-4742-bb41-b7d72e4a0941/GCF_014191785.1_ASM1419178v1_genomic.fna.gz | prodigal -d GCF_014191785.1_ASM1419178v1_genomic.fna/cds.fna -a GCF_014191785.1_ASM1419178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:46,044] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:46,044] [INFO] Task started: HMMsearch
[2024-01-24 13:56:46,045] [INFO] Running command: hmmsearch --tblout GCF_014191785.1_ASM1419178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference/reference_markers.hmm GCF_014191785.1_ASM1419178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:46,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:46,377] [INFO] Found 6/6 markers.
[2024-01-24 13:56:46,431] [INFO] Query marker FASTA was written to GCF_014191785.1_ASM1419178v1_genomic.fna/markers.fasta
[2024-01-24 13:56:46,431] [INFO] Task started: Blastn
[2024-01-24 13:56:46,431] [INFO] Running command: blastn -query GCF_014191785.1_ASM1419178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference/reference_markers.fasta -out GCF_014191785.1_ASM1419178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:47,021] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:47,025] [INFO] Selected 17 target genomes.
[2024-01-24 13:56:47,025] [INFO] Target genome list was writen to GCF_014191785.1_ASM1419178v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:47,035] [INFO] Task started: fastANI
[2024-01-24 13:56:47,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg36a05de3-a430-4742-bb41-b7d72e4a0941/GCF_014191785.1_ASM1419178v1_genomic.fna.gz --refList GCF_014191785.1_ASM1419178v1_genomic.fna/target_genomes.txt --output GCF_014191785.1_ASM1419178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:05,661] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:05,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:05,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:05,676] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:05,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:05,676] [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 baekrokdamisoli	strain=CECT 8890	GCA_014191785.1	1712516	1712516	type	True	100.0	2363	2364	95	conclusive
Paenibacillus baekrokdamisoli	strain=KCTC 33723	GCA_003945345.1	1712516	1712516	type	True	99.9991	2363	2364	95	conclusive
Paenibacillus luteus	strain=R-3	GCA_006542765.1	2545753	2545753	type	True	78.4225	223	2364	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	78.2391	326	2364	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	78.0419	100	2364	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	78.0053	305	2364	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.9684	263	2364	95	below_threshold
Paenibacillus oenotherae	strain=DT7-4	GCA_019443105.1	1435645	1435645	type	True	77.7787	269	2364	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	77.3998	186	2364	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	77.2021	54	2364	95	below_threshold
Paenibacillus gallinarum	strain=Sa2BVA9	GCA_014836635.1	2762232	2762232	type	True	77.107	69	2364	95	below_threshold
Paenibacillus abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	77.0175	143	2364	95	below_threshold
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	76.5951	119	2364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:05,678] [INFO] DFAST Taxonomy check result was written to GCF_014191785.1_ASM1419178v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:05,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:05,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:05,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference/checkm_data
[2024-01-24 13:57:05,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:05,744] [INFO] Task started: CheckM
[2024-01-24 13:57:05,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191785.1_ASM1419178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191785.1_ASM1419178v1_genomic.fna/checkm_input GCF_014191785.1_ASM1419178v1_genomic.fna/checkm_result
[2024-01-24 13:58:00,909] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:00,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:00,936] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:00,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:00,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191785.1_ASM1419178v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:00,937] [INFO] Task started: Blastn
[2024-01-24 13:58:00,937] [INFO] Running command: blastn -query GCF_014191785.1_ASM1419178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa8811f6-a563-4d61-9fe0-4d8f04c7234b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191785.1_ASM1419178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:01,801] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:01,805] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:01,806] [INFO] Target genome list was writen to GCF_014191785.1_ASM1419178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:01,821] [INFO] Task started: fastANI
[2024-01-24 13:58:01,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg36a05de3-a430-4742-bb41-b7d72e4a0941/GCF_014191785.1_ASM1419178v1_genomic.fna.gz --refList GCF_014191785.1_ASM1419178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191785.1_ASM1419178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:28,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:28,460] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:28,461] [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_003945345.1	s__Paenibacillus_Z baekrokdamisoli	99.9991	2363	2364	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001280845.1	s__Paenibacillus_C sp001280845	79.2	232	2364	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_900106745.1	s__Paenibacillus_Z sp900106745	78.4841	306	2364	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_900116125.1	s__Paenibacillus_Z sp900116125	78.1222	309	2364	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	95.31	95.31	0.87	0.87	2	-
GCF_016908135.1	s__Paenibacillus_Z mendelii	78.074	304	2364	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_001956095.1	s__Paenibacillus_C sp001956095	78.0308	175	2364	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_003268025.1	s__Paenibacillus_Z montanisoli	77.9684	263	2364	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_010365285.1	s__Paenibacillus_Z rhizovicinus	77.9557	270	2364	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_001956295.1	s__Paenibacillus_C sp001956295	77.8243	213	2364	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_001428245.1	s__Paenibacillus_C sp001428245	77.779	209	2364	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_017874275.1	s__Paenibacillus_Z sepulcri	77.698	306	2364	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_016019935.1	s__Paenibacillus_C sp016019935	77.5728	118	2364	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_001682865.1	s__Paenibacillus_C sp001682865	77.5203	210	2364	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.12	99.12	0.94	0.94	2	-
GCF_014192395.1	s__Paenibacillus_C endophyticus	77.4611	180	2364	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_014192105.1	s__Paenibacillus_Z phyllosphaerae	77.4162	185	2364	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_011761355.1	s__Paenibacillus_C lupini	77.2567	165	2364	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_009737085.1	s__Paenibacillus_C sp009737085	77.115	134	2364	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_008124765.1	s__Paenibacillus_Z methanolicus	77.0556	178	2364	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_014640295.1	s__Paenibacillus_D abyssi	77.0012	143	2364	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000825.1	s__Paenibacillus_T kobensis	76.6122	119	2364	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570725.1	s__Paenibacillus amylolyticus_A	76.5803	83	2364	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.59	97.52	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:28,462] [INFO] GTDB search result was written to GCF_014191785.1_ASM1419178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:28,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:28,469] [INFO] DFAST_QC result json was written to GCF_014191785.1_ASM1419178v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:28,469] [INFO] DFAST_QC completed!
[2024-01-24 13:58:28,469] [INFO] Total running time: 0h2m1s