[2024-01-25 18:46:50,869] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:50,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:50,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference
[2024-01-25 18:46:52,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:52,064] [INFO] Task started: Prodigal
[2024-01-25 18:46:52,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d194445-a260-4640-b24c-fc883d4c2a10/GCF_000422445.1_ASM42244v1_genomic.fna.gz | prodigal -d GCF_000422445.1_ASM42244v1_genomic.fna/cds.fna -a GCF_000422445.1_ASM42244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:03,035] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:03,035] [INFO] Task started: HMMsearch
[2024-01-25 18:47:03,035] [INFO] Running command: hmmsearch --tblout GCF_000422445.1_ASM42244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference/reference_markers.hmm GCF_000422445.1_ASM42244v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:03,345] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:03,346] [INFO] Found 6/6 markers.
[2024-01-25 18:47:03,386] [INFO] Query marker FASTA was written to GCF_000422445.1_ASM42244v1_genomic.fna/markers.fasta
[2024-01-25 18:47:03,386] [INFO] Task started: Blastn
[2024-01-25 18:47:03,387] [INFO] Running command: blastn -query GCF_000422445.1_ASM42244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference/reference_markers.fasta -out GCF_000422445.1_ASM42244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:03,959] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:03,962] [INFO] Selected 17 target genomes.
[2024-01-25 18:47:03,962] [INFO] Target genome list was writen to GCF_000422445.1_ASM42244v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:03,971] [INFO] Task started: fastANI
[2024-01-25 18:47:03,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d194445-a260-4640-b24c-fc883d4c2a10/GCF_000422445.1_ASM42244v1_genomic.fna.gz --refList GCF_000422445.1_ASM42244v1_genomic.fna/target_genomes.txt --output GCF_000422445.1_ASM42244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:19,215] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:19,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:19,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:19,227] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:19,227] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:19,228] [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 assamensis	strain=DSM 18201	GCA_000422445.1	311244	311244	type	True	100.0	1654	1658	95	conclusive
Paenibacillus arenosi	strain=CAU 1523	GCA_014841135.1	2774142	2774142	type	True	93.4498	1472	1658	95	below_threshold
Paenibacillus aquistagni	strain=11	GCA_900177815.1	1852522	1852522	type	True	79.1542	171	1658	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	78.5794	151	1658	95	below_threshold
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	78.3337	146	1658	95	below_threshold
Paenibacillus thiaminolyticus	strain=NBRC 15656	GCA_004001005.1	49283	49283	type	True	77.98	141	1658	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	77.2304	62	1658	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.1318	79	1658	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	76.962	84	1658	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	76.8621	91	1658	95	below_threshold
Paenibacillus etheri	strain=SH7	GCA_001012825.2	1306852	1306852	type	True	76.7174	70	1658	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	76.6378	68	1658	95	below_threshold
Paenibacillus sediminis	strain=DSM 23491	GCA_017873765.1	664909	664909	type	True	76.236	66	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:19,229] [INFO] DFAST Taxonomy check result was written to GCF_000422445.1_ASM42244v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:19,231] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:19,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:19,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference/checkm_data
[2024-01-25 18:47:19,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:19,283] [INFO] Task started: CheckM
[2024-01-25 18:47:19,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422445.1_ASM42244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422445.1_ASM42244v1_genomic.fna/checkm_input GCF_000422445.1_ASM42244v1_genomic.fna/checkm_result
[2024-01-25 18:47:54,648] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:54,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:54,667] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:54,668] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:54,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422445.1_ASM42244v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:54,668] [INFO] Task started: Blastn
[2024-01-25 18:47:54,668] [INFO] Running command: blastn -query GCF_000422445.1_ASM42244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f5ee0b9-b867-4863-a8ea-d24ac8b99190/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422445.1_ASM42244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:55,403] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:55,407] [INFO] Selected 14 target genomes.
[2024-01-25 18:47:55,407] [INFO] Target genome list was writen to GCF_000422445.1_ASM42244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:55,423] [INFO] Task started: fastANI
[2024-01-25 18:47:55,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d194445-a260-4640-b24c-fc883d4c2a10/GCF_000422445.1_ASM42244v1_genomic.fna.gz --refList GCF_000422445.1_ASM42244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422445.1_ASM42244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:10,289] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:10,297] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:10,297] [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_000422445.1	s__Paenibacillus_B assamensis	100.0	1654	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014841135.1	s__Paenibacillus_B sp014841135	93.4498	1472	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786455.1	s__Paenibacillus_B sp007786455	88.3139	1420	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177815.1	s__Paenibacillus_B aquistagni	79.2055	168	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.59	98.22	0.95	0.95	3	-
GCF_007066085.1	s__Paenibacillus_B thiaminolyticus	78.6156	148	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.67	95.07	0.96	0.85	7	-
GCF_000245555.1	s__Paenibacillus_B dendritiformis_A	78.3225	121	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	97.57	96.94	0.92	0.90	3	-
GCF_000425125.1	s__Paenibacillus_B taiwanensis	77.9818	202	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894745.1	s__Paenibacillus_B sp001894745	77.826	189	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	96.43	95.29	0.89	0.85	9	-
GCF_017052585.1	s__Paenibacillus_B apiarius	77.5686	170	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.54	98.54	0.95	0.95	2	-
GCF_001012825.1	s__Paenibacillus etheri	76.8463	66	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426545.1	s__Paenibacillus panacisoli	76.7833	54	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	96.1083	98.22	98.22	0.93	0.93	2	-
GCF_003994465.1	s__Paenibacillus_A zeisoli	76.6308	65	1658	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:10,298] [INFO] GTDB search result was written to GCF_000422445.1_ASM42244v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:10,299] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:10,301] [INFO] DFAST_QC result json was written to GCF_000422445.1_ASM42244v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:10,302] [INFO] DFAST_QC completed!
[2024-01-25 18:48:10,302] [INFO] Total running time: 0h1m19s