[2024-01-24 11:51:36,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,070] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,070] [INFO] DQC Reference Directory: /var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference
[2024-01-24 11:51:37,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:37,346] [INFO] Task started: Prodigal
[2024-01-24 11:51:37,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ade84f4-b866-4642-9983-a3385dbbe6cd/GCF_004001005.1_ASM400100v1_genomic.fna.gz | prodigal -d GCF_004001005.1_ASM400100v1_genomic.fna/cds.fna -a GCF_004001005.1_ASM400100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:55,174] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:55,175] [INFO] Task started: HMMsearch
[2024-01-24 11:51:55,175] [INFO] Running command: hmmsearch --tblout GCF_004001005.1_ASM400100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference/reference_markers.hmm GCF_004001005.1_ASM400100v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:55,519] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:55,521] [INFO] Found 6/6 markers.
[2024-01-24 11:51:55,573] [INFO] Query marker FASTA was written to GCF_004001005.1_ASM400100v1_genomic.fna/markers.fasta
[2024-01-24 11:51:55,574] [INFO] Task started: Blastn
[2024-01-24 11:51:55,574] [INFO] Running command: blastn -query GCF_004001005.1_ASM400100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference/reference_markers.fasta -out GCF_004001005.1_ASM400100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:56,197] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:56,201] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:56,202] [INFO] Target genome list was writen to GCF_004001005.1_ASM400100v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:56,208] [INFO] Task started: fastANI
[2024-01-24 11:51:56,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ade84f4-b866-4642-9983-a3385dbbe6cd/GCF_004001005.1_ASM400100v1_genomic.fna.gz --refList GCF_004001005.1_ASM400100v1_genomic.fna/target_genomes.txt --output GCF_004001005.1_ASM400100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:11,026] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:11,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:11,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:11,050] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:52:11,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:11,050] [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 thiaminolyticus	strain=NBRC 15656	GCA_004001005.1	49283	49283	type	True	100.0	2041	2052	95	conclusive
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_002161855.1	49283	49283	type	True	99.9989	2052	2052	95	conclusive
Paenibacillus thiaminolyticus	strain=NRRL B-4156	GCA_007066085.1	49283	49283	type	True	99.9988	2052	2052	95	conclusive
Paenibacillus popilliae	strain=ATCC 14706	GCA_000315235.1	78057	78057	type	True	88.7738	855	2052	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	76.7156	143	2052	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.6416	103	2052	95	below_threshold
Paenibacillus ginsengihumi	strain=DSM 21568	GCA_000380965.1	431596	431596	type	True	76.6056	158	2052	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	76.5505	173	2052	95	below_threshold
Paenibacillus cisolokensis	strain=LC2-13A	GCA_018403665.1	1658519	1658519	type	True	76.4606	188	2052	95	below_threshold
Paenibacillus paeoniae	strain=M4BSY-1	GCA_003388735.1	2292705	2292705	type	True	76.3378	93	2052	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	76.3181	124	2052	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.2351	102	2052	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	76.1896	131	2052	95	below_threshold
Paenibacillus glycanilyticus	strain=NBRC 16618	GCA_004000805.1	126569	126569	type	True	76.012	117	2052	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	75.9094	88	2052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:11,052] [INFO] DFAST Taxonomy check result was written to GCF_004001005.1_ASM400100v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:11,053] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:11,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:11,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference/checkm_data
[2024-01-24 11:52:11,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:11,158] [INFO] Task started: CheckM
[2024-01-24 11:52:11,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004001005.1_ASM400100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004001005.1_ASM400100v1_genomic.fna/checkm_input GCF_004001005.1_ASM400100v1_genomic.fna/checkm_result
[2024-01-24 11:53:03,938] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:03,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:03,960] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:03,961] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:03,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004001005.1_ASM400100v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:03,962] [INFO] Task started: Blastn
[2024-01-24 11:53:03,962] [INFO] Running command: blastn -query GCF_004001005.1_ASM400100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee5e7101-3f75-4610-a87a-48e3ef30a9ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_004001005.1_ASM400100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:04,805] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:04,808] [INFO] Selected 6 target genomes.
[2024-01-24 11:53:04,808] [INFO] Target genome list was writen to GCF_004001005.1_ASM400100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:04,814] [INFO] Task started: fastANI
[2024-01-24 11:53:04,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ade84f4-b866-4642-9983-a3385dbbe6cd/GCF_004001005.1_ASM400100v1_genomic.fna.gz --refList GCF_004001005.1_ASM400100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004001005.1_ASM400100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:13,637] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:13,646] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:13,646] [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_007066085.1	s__Paenibacillus_B thiaminolyticus	99.9988	2052	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	98.67	95.07	0.96	0.85	7	conclusive
GCF_000245555.1	s__Paenibacillus_B dendritiformis_A	92.7953	1686	2052	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_018403065.1	s__Paenibacillus_B dendritiformis_B	91.2572	1551	2052	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_015845845.1	s__Paenibacillus_B dendritiformis_C	91.0039	1555	2052	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_013266915.1	s__Paenibacillus_B sp900539405	90.609	1631	2052	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_B	95.0	99.54	99.32	0.96	0.95	4	-
GCF_000315235.1	s__Paenibacillus_B popilliae	88.7541	856	2052	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 11:53:13,647] [INFO] GTDB search result was written to GCF_004001005.1_ASM400100v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:13,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:13,651] [INFO] DFAST_QC result json was written to GCF_004001005.1_ASM400100v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:13,651] [INFO] DFAST_QC completed!
[2024-01-24 11:53:13,651] [INFO] Total running time: 0h1m38s