[2024-01-24 11:05:03,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,934] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,815] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2a05964-e40a-4d4d-a807-5f448f79a2a3/GCF_009807035.1_ASM980703v1_genomic.fna.gz | prodigal -d GCF_009807035.1_ASM980703v1_genomic.fna/cds.fna -a GCF_009807035.1_ASM980703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:24,757] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:24,758] [INFO] Task started: HMMsearch
[2024-01-24 11:05:24,758] [INFO] Running command: hmmsearch --tblout GCF_009807035.1_ASM980703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference/reference_markers.hmm GCF_009807035.1_ASM980703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:25,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:25,084] [INFO] Found 6/6 markers.
[2024-01-24 11:05:25,131] [INFO] Query marker FASTA was written to GCF_009807035.1_ASM980703v1_genomic.fna/markers.fasta
[2024-01-24 11:05:25,131] [INFO] Task started: Blastn
[2024-01-24 11:05:25,131] [INFO] Running command: blastn -query GCF_009807035.1_ASM980703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference/reference_markers.fasta -out GCF_009807035.1_ASM980703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:25,693] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:25,695] [INFO] Selected 20 target genomes.
[2024-01-24 11:05:25,695] [INFO] Target genome list was writen to GCF_009807035.1_ASM980703v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:25,701] [INFO] Task started: fastANI
[2024-01-24 11:05:25,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a05964-e40a-4d4d-a807-5f448f79a2a3/GCF_009807035.1_ASM980703v1_genomic.fna.gz --refList GCF_009807035.1_ASM980703v1_genomic.fna/target_genomes.txt --output GCF_009807035.1_ASM980703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:46,778] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:46,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:46,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:46,790] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:46,790] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:46,791] [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 dokdonensis	strain=YH-JAE5	GCA_004916975.1	2567944	2567944	type	True	83.2334	1405	2204	95	below_threshold
Paenibacillus chibensis	strain=NBRC 15958	GCA_004001045.1	59846	59846	type	True	82.5996	1204	2204	95	below_threshold
Paenibacillus rhizosphaerae	strain=CECT 5831	GCA_014192015.1	297318	297318	type	True	79.4601	570	2204	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	78.759	240	2204	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	78.6948	349	2204	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	78.077	319	2204	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	77.6882	248	2204	95	below_threshold
Paenibacillus pabuli	strain=NBRC 13638	GCA_001514495.1	1472	1472	suspected-type	True	77.5996	209	2204	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	77.544	207	2204	95	below_threshold
Paenibacillus sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	77.526	137	2204	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.3367	178	2204	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.3203	148	2204	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	77.302	180	2204	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	77.1832	129	2204	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.1823	151	2204	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	77.1721	187	2204	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	77.1335	196	2204	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.0729	189	2204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:46,792] [INFO] DFAST Taxonomy check result was written to GCF_009807035.1_ASM980703v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:46,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:46,793] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:46,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference/checkm_data
[2024-01-24 11:05:46,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:46,855] [INFO] Task started: CheckM
[2024-01-24 11:05:46,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009807035.1_ASM980703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009807035.1_ASM980703v1_genomic.fna/checkm_input GCF_009807035.1_ASM980703v1_genomic.fna/checkm_result
[2024-01-24 11:06:43,872] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:43,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:43,889] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:43,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:43,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009807035.1_ASM980703v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:43,889] [INFO] Task started: Blastn
[2024-01-24 11:06:43,889] [INFO] Running command: blastn -query GCF_009807035.1_ASM980703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e79ef3-78b1-4ef2-ba53-dccb4c1f2a26/dqc_reference/reference_markers_gtdb.fasta -out GCF_009807035.1_ASM980703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:44,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:44,664] [INFO] Selected 9 target genomes.
[2024-01-24 11:06:44,664] [INFO] Target genome list was writen to GCF_009807035.1_ASM980703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:44,669] [INFO] Task started: fastANI
[2024-01-24 11:06:44,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a05964-e40a-4d4d-a807-5f448f79a2a3/GCF_009807035.1_ASM980703v1_genomic.fna.gz --refList GCF_009807035.1_ASM980703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009807035.1_ASM980703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:56,123] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:56,130] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:56,130] [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_009807035.1	s__Paenibacillus sp009807035	100.0	2203	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018403225.1	s__Paenibacillus sp018403225	83.3261	1390	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916975.1	s__Paenibacillus dokdonensis	83.2357	1404	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001045.1	s__Paenibacillus chibensis	82.5947	1205	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333315.1	s__Paenibacillus azoreducens	80.5654	950	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_009870825.1	s__Paenibacillus albilobatus	80.3293	941	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.80	99.80	0.98	0.98	2	-
GCF_018333375.1	s__Paenibacillus cookii	80.315	899	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
GCF_002272015.1	s__Paenibacillus campinasensis	77.5231	208	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	77.2814	179	2204	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:56,131] [INFO] GTDB search result was written to GCF_009807035.1_ASM980703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:56,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:56,134] [INFO] DFAST_QC result json was written to GCF_009807035.1_ASM980703v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:56,134] [INFO] DFAST_QC completed!
[2024-01-24 11:06:56,134] [INFO] Total running time: 0h1m52s