[2024-01-24 12:29:39,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:39,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:39,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference
[2024-01-24 12:29:42,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:42,402] [INFO] Task started: Prodigal
[2024-01-24 12:29:42,403] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6bb5b47-c523-41ba-8082-678d54c9917c/GCF_001637335.1_ASM163733v1_genomic.fna.gz | prodigal -d GCF_001637335.1_ASM163733v1_genomic.fna/cds.fna -a GCF_001637335.1_ASM163733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:52,375] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:52,375] [INFO] Task started: HMMsearch
[2024-01-24 12:29:52,376] [INFO] Running command: hmmsearch --tblout GCF_001637335.1_ASM163733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference/reference_markers.hmm GCF_001637335.1_ASM163733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:52,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:52,650] [INFO] Found 6/6 markers.
[2024-01-24 12:29:52,694] [INFO] Query marker FASTA was written to GCF_001637335.1_ASM163733v1_genomic.fna/markers.fasta
[2024-01-24 12:29:52,694] [INFO] Task started: Blastn
[2024-01-24 12:29:52,694] [INFO] Running command: blastn -query GCF_001637335.1_ASM163733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference/reference_markers.fasta -out GCF_001637335.1_ASM163733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:53,266] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:53,270] [INFO] Selected 13 target genomes.
[2024-01-24 12:29:53,271] [INFO] Target genome list was writen to GCF_001637335.1_ASM163733v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:53,279] [INFO] Task started: fastANI
[2024-01-24 12:29:53,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6bb5b47-c523-41ba-8082-678d54c9917c/GCF_001637335.1_ASM163733v1_genomic.fna.gz --refList GCF_001637335.1_ASM163733v1_genomic.fna/target_genomes.txt --output GCF_001637335.1_ASM163733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:04,909] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:04,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:04,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:04,919] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:30:04,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:04,920] [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 crassostreae	strain=LPB0068	GCA_001637335.1	1763538	1763538	type	True	100.0	1533	1534	95	conclusive
Paenibacillus crassostreae	strain=LPB0068	GCA_001857945.1	1763538	1763538	type	True	99.9966	1534	1534	95	conclusive
Paenibacillus glacialis	strain=DSM 22343	GCA_001637205.1	494026	494026	type	True	79.6102	597	1534	95	below_threshold
Paenibacillus macquariensis subsp. macquariensis	strain=DSM 2	GCA_001637165.1	1468	948756	type	True	79.565	553	1534	95	below_threshold
Paenibacillus macquariensis	strain=ATCC 23464	GCA_900156375.1	948756	948756	type	True	79.4784	564	1534	95	below_threshold
Paenibacillus antarcticus	strain=CECT 5836	GCA_001637225.1	253703	253703	type	True	79.4587	565	1534	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.8883	103	1534	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	77.7854	134	1534	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:04,925] [INFO] DFAST Taxonomy check result was written to GCF_001637335.1_ASM163733v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:04,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:04,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:04,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference/checkm_data
[2024-01-24 12:30:04,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:04,981] [INFO] Task started: CheckM
[2024-01-24 12:30:04,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001637335.1_ASM163733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001637335.1_ASM163733v1_genomic.fna/checkm_input GCF_001637335.1_ASM163733v1_genomic.fna/checkm_result
[2024-01-24 12:30:39,562] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:39,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:39,588] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:39,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:39,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001637335.1_ASM163733v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:39,590] [INFO] Task started: Blastn
[2024-01-24 12:30:39,590] [INFO] Running command: blastn -query GCF_001637335.1_ASM163733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c97fbd2-8bba-4165-bd77-ae300fa95ae5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001637335.1_ASM163733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:40,318] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:40,323] [INFO] Selected 11 target genomes.
[2024-01-24 12:30:40,323] [INFO] Target genome list was writen to GCF_001637335.1_ASM163733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:40,332] [INFO] Task started: fastANI
[2024-01-24 12:30:40,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6bb5b47-c523-41ba-8082-678d54c9917c/GCF_001637335.1_ASM163733v1_genomic.fna.gz --refList GCF_001637335.1_ASM163733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001637335.1_ASM163733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:51,748] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:51,772] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:51,773] [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_001857945.1	s__Paenibacillus crassostreae	99.9966	1534	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001637205.1	s__Paenibacillus glacialis	79.6157	595	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156375.1	s__Paenibacillus macquariensis	79.4784	564	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.68	95.38	0.90	0.81	3	-
GCF_001637225.1	s__Paenibacillus antarcticus	79.458	565	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000949425.1	s__Paenibacillus sp000949425	78.7304	369	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758725.1	s__Paenibacillus odorifer	77.8106	133	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
GCF_000576305.1	s__Paenibacillus pini	77.7423	184	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002264395.1	s__Paenibacillus sp002264395	77.7297	122	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
GCF_900116105.1	s__Paenibacillus sp900116105	77.2216	95	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102085.1	s__Paenibacillus polysaccharolyticus	77.1945	79	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.73	97.72	0.92	0.92	4	-
GCF_016908805.1	s__Paenibacillus_J nicotianae	76.7484	94	1534	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:51,776] [INFO] GTDB search result was written to GCF_001637335.1_ASM163733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:51,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:51,782] [INFO] DFAST_QC result json was written to GCF_001637335.1_ASM163733v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:51,782] [INFO] DFAST_QC completed!
[2024-01-24 12:30:51,782] [INFO] Total running time: 0h1m12s