[2024-01-24 14:06:07,079] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,082] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference
[2024-01-24 14:06:08,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,528] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,528] [INFO] Running command: gunzip -c /var/lib/cwl/stg2385fb98-210d-46b6-94d8-19c778be9102/GCF_003182255.1_ASM318225v1_genomic.fna.gz | prodigal -d GCF_003182255.1_ASM318225v1_genomic.fna/cds.fna -a GCF_003182255.1_ASM318225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:28,308] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:28,308] [INFO] Task started: HMMsearch
[2024-01-24 14:06:28,308] [INFO] Running command: hmmsearch --tblout GCF_003182255.1_ASM318225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference/reference_markers.hmm GCF_003182255.1_ASM318225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:28,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:28,706] [INFO] Found 6/6 markers.
[2024-01-24 14:06:28,774] [INFO] Query marker FASTA was written to GCF_003182255.1_ASM318225v1_genomic.fna/markers.fasta
[2024-01-24 14:06:28,775] [INFO] Task started: Blastn
[2024-01-24 14:06:28,775] [INFO] Running command: blastn -query GCF_003182255.1_ASM318225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference/reference_markers.fasta -out GCF_003182255.1_ASM318225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:29,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:29,455] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:29,455] [INFO] Target genome list was writen to GCF_003182255.1_ASM318225v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:29,462] [INFO] Task started: fastANI
[2024-01-24 14:06:29,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg2385fb98-210d-46b6-94d8-19c778be9102/GCF_003182255.1_ASM318225v1_genomic.fna.gz --refList GCF_003182255.1_ASM318225v1_genomic.fna/target_genomes.txt --output GCF_003182255.1_ASM318225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:49,967] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:49,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:49,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:49,983] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:49,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:49,983] [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 cellulosilyticus	strain=CECT 5696	GCA_003182255.1	375489	375489	type	True	100.0	2284	2286	95	conclusive
Paenibacillus kobensis	strain=NBRC 15729	GCA_004000825.1	59841	59841	type	True	79.716	674	2286	95	below_threshold
Paenibacillus curdlanolyticus	strain=YK9	GCA_000179615.1	59840	59840	type	True	79.3272	499	2286	95	below_threshold
Paenibacillus xylaniclasticus	strain=NBRC 106381	GCA_004001065.1	588083	588083	type	True	79.1495	462	2286	95	below_threshold
Paenibacillus phyllosphaerae	strain=CECT 5862	GCA_014192105.1	274593	274593	type	True	77.5587	306	2286	95	below_threshold
Paenibacillus glycanilyticus subsp. hiroshimensis	strain=CCI5	GCA_015473105.1	2805378	126569	type	True	77.4939	296	2286	95	below_threshold
Paenibacillus gorillae		GCA_000513275.1	1243662	1243662	type	True	77.4489	198	2286	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	77.39	297	2286	95	below_threshold
Paenibacillus lignilyticus	strain=DLE-14	GCA_017942085.1	1172615	1172615	type	True	77.2673	201	2286	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	77.2149	230	2286	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	77.0129	166	2286	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.8434	230	2286	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.8363	178	2286	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.7198	125	2286	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.6279	171	2286	95	below_threshold
Paenibacillus terrigena	strain=DSM 21567	GCA_000374845.1	369333	369333	type	True	76.3837	102	2286	95	below_threshold
Paenibacillus oceani	strain=IB182363	GCA_014705615.1	2772510	2772510	type	True	76.2745	108	2286	95	below_threshold
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	76.1583	72	2286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:49,985] [INFO] DFAST Taxonomy check result was written to GCF_003182255.1_ASM318225v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:49,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:49,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:49,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference/checkm_data
[2024-01-24 14:06:49,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:50,052] [INFO] Task started: CheckM
[2024-01-24 14:06:50,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182255.1_ASM318225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182255.1_ASM318225v1_genomic.fna/checkm_input GCF_003182255.1_ASM318225v1_genomic.fna/checkm_result
[2024-01-24 14:07:45,125] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:45,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:45,144] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:45,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:45,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182255.1_ASM318225v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:45,146] [INFO] Task started: Blastn
[2024-01-24 14:07:45,146] [INFO] Running command: blastn -query GCF_003182255.1_ASM318225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3b783d-8c59-4dcd-93d4-79c2e0c39f5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182255.1_ASM318225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:45,937] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:45,940] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:45,940] [INFO] Target genome list was writen to GCF_003182255.1_ASM318225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:45,952] [INFO] Task started: fastANI
[2024-01-24 14:07:45,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg2385fb98-210d-46b6-94d8-19c778be9102/GCF_003182255.1_ASM318225v1_genomic.fna.gz --refList GCF_003182255.1_ASM318225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182255.1_ASM318225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:00,844] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:00,868] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:00,868] [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_003182255.1	s__Paenibacillus_T cellulosilyticus	100.0	2284	2286	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014779765.1	s__Paenibacillus_T sp014779765	84.6295	1473	2286	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_004000825.1	s__Paenibacillus_T kobensis	79.7234	673	2286	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_000179615.1	s__Paenibacillus_T curdlanolyticus	79.3165	500	2286	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_004001065.1	s__Paenibacillus_T xylaniclasticus	79.1649	460	2286	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009789195.1	s__Paenibacillus_T sp009789195	79.1435	486	2286	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_000023585.1	s__Paenibacillus_C sp000023585	77.7595	275	2286	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_004342525.1	s__Paenibacillus_Z sp004342525	77.5864	255	2286	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_003591485.1	s__Paenibacillus_C sp003591485	77.4649	191	2286	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	77.4412	200	2286	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_004000805.1	s__Paenibacillus_C glycanilyticus	77.39	297	2286	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	97.79	97.79	0.90	0.90	2	-
GCF_003217535.1	s__Paenibacillus_C sp003217535	77.2571	164	2286	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_015845845.1	s__Paenibacillus_B dendritiformis_C	76.2399	104	2286	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:00,870] [INFO] GTDB search result was written to GCF_003182255.1_ASM318225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:00,870] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:00,874] [INFO] DFAST_QC result json was written to GCF_003182255.1_ASM318225v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:00,874] [INFO] DFAST_QC completed!
[2024-01-24 14:08:00,874] [INFO] Total running time: 0h1m54s