[2024-01-25 19:55:05,565] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:05,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:05,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference
[2024-01-25 19:55:06,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:06,699] [INFO] Task started: Prodigal
[2024-01-25 19:55:06,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgce9086c8-291c-45ea-ae8a-7e7c82721ea1/GCF_013141775.1_ASM1314177v1_genomic.fna.gz | prodigal -d GCF_013141775.1_ASM1314177v1_genomic.fna/cds.fna -a GCF_013141775.1_ASM1314177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:25,482] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:25,483] [INFO] Task started: HMMsearch
[2024-01-25 19:55:25,483] [INFO] Running command: hmmsearch --tblout GCF_013141775.1_ASM1314177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference/reference_markers.hmm GCF_013141775.1_ASM1314177v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:25,833] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:25,834] [INFO] Found 6/6 markers.
[2024-01-25 19:55:25,895] [INFO] Query marker FASTA was written to GCF_013141775.1_ASM1314177v1_genomic.fna/markers.fasta
[2024-01-25 19:55:25,895] [INFO] Task started: Blastn
[2024-01-25 19:55:25,895] [INFO] Running command: blastn -query GCF_013141775.1_ASM1314177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference/reference_markers.fasta -out GCF_013141775.1_ASM1314177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:26,474] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:26,477] [INFO] Selected 11 target genomes.
[2024-01-25 19:55:26,477] [INFO] Target genome list was writen to GCF_013141775.1_ASM1314177v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:26,483] [INFO] Task started: fastANI
[2024-01-25 19:55:26,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9086c8-291c-45ea-ae8a-7e7c82721ea1/GCF_013141775.1_ASM1314177v1_genomic.fna.gz --refList GCF_013141775.1_ASM1314177v1_genomic.fna/target_genomes.txt --output GCF_013141775.1_ASM1314177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:45,179] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:45,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:45,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:45,187] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:45,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:45,188] [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 phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	100.0	2772	2776	95	conclusive
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	92.7633	2288	2776	95	below_threshold
Paenibacillus tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	85.1922	1740	2776	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	83.7219	1702	2776	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	82.3345	1544	2776	95	below_threshold
Paenibacillus riograndensis	strain=SBR5	GCA_000224945.2	483937	483937	type	True	81.1997	899	2776	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	81.1751	1076	2776	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	81.1534	1251	2776	95	below_threshold
Paenibacillus ihuae	strain=GD6	GCA_001368795.1	1232431	1232431	type	True	80.9525	1161	2776	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.4433	660	2776	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.0718	467	2776	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:45,189] [INFO] DFAST Taxonomy check result was written to GCF_013141775.1_ASM1314177v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:45,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:45,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:45,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference/checkm_data
[2024-01-25 19:55:45,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:45,267] [INFO] Task started: CheckM
[2024-01-25 19:55:45,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013141775.1_ASM1314177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013141775.1_ASM1314177v1_genomic.fna/checkm_input GCF_013141775.1_ASM1314177v1_genomic.fna/checkm_result
[2024-01-25 19:56:40,097] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:40,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:40,119] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:40,119] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:40,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013141775.1_ASM1314177v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:40,120] [INFO] Task started: Blastn
[2024-01-25 19:56:40,120] [INFO] Running command: blastn -query GCF_013141775.1_ASM1314177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66d735b4-9ad5-4413-a63f-2345c52313c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013141775.1_ASM1314177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:40,952] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:40,960] [INFO] Selected 7 target genomes.
[2024-01-25 19:56:40,960] [INFO] Target genome list was writen to GCF_013141775.1_ASM1314177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:40,972] [INFO] Task started: fastANI
[2024-01-25 19:56:40,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9086c8-291c-45ea-ae8a-7e7c82721ea1/GCF_013141775.1_ASM1314177v1_genomic.fna.gz --refList GCF_013141775.1_ASM1314177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013141775.1_ASM1314177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:54,822] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:54,827] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:54,827] [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_013141775.1	s__Paenibacillus phytohabitans	100.0	2772	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	conclusive
GCF_000758605.1	s__Paenibacillus sp000758605	94.4324	2062	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758665.1	s__Paenibacillus borealis	92.7669	2287	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204885.1	s__Paenibacillus tritici	85.2	1739	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	-
GCF_017874765.1	s__Paenibacillus rhizoplanae	83.9355	1646	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874735.1	s__Paenibacillus silagei	83.7346	1699	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_001955925.1	s__Paenibacillus sp001955925	83.4864	1601	2776	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:54,829] [INFO] GTDB search result was written to GCF_013141775.1_ASM1314177v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:54,829] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:54,832] [INFO] DFAST_QC result json was written to GCF_013141775.1_ASM1314177v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:54,832] [INFO] DFAST_QC completed!
[2024-01-25 19:56:54,832] [INFO] Total running time: 0h1m49s