[2024-01-24 11:26:27,675] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference
[2024-01-24 11:26:29,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,114] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg30dcda76-d180-44f0-ab56-7552a8995c4e/GCF_003994475.1_ASM399447v1_genomic.fna.gz | prodigal -d GCF_003994475.1_ASM399447v1_genomic.fna/cds.fna -a GCF_003994475.1_ASM399447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:43,200] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:43,200] [INFO] Task started: HMMsearch
[2024-01-24 11:26:43,200] [INFO] Running command: hmmsearch --tblout GCF_003994475.1_ASM399447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference/reference_markers.hmm GCF_003994475.1_ASM399447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:43,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:43,642] [INFO] Found 6/6 markers.
[2024-01-24 11:26:43,688] [INFO] Query marker FASTA was written to GCF_003994475.1_ASM399447v1_genomic.fna/markers.fasta
[2024-01-24 11:26:43,688] [INFO] Task started: Blastn
[2024-01-24 11:26:43,688] [INFO] Running command: blastn -query GCF_003994475.1_ASM399447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference/reference_markers.fasta -out GCF_003994475.1_ASM399447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:44,271] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:44,274] [INFO] Selected 27 target genomes.
[2024-01-24 11:26:44,274] [INFO] Target genome list was writen to GCF_003994475.1_ASM399447v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:44,284] [INFO] Task started: fastANI
[2024-01-24 11:26:44,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg30dcda76-d180-44f0-ab56-7552a8995c4e/GCF_003994475.1_ASM399447v1_genomic.fna.gz --refList GCF_003994475.1_ASM399447v1_genomic.fna/target_genomes.txt --output GCF_003994475.1_ASM399447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:09,507] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:09,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:09,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:09,523] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:09,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:09,524] [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 anaericanus	strain=DSM 15890	GCA_003994475.1	170367	170367	type	True	100.0	1974	1980	95	conclusive
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	82.3117	1159	1980	95	below_threshold
Paenibacillus lutimineralis	strain=MBLB1234	GCA_003991425.1	2707005	2707005	type	True	78.6304	267	1980	95	below_threshold
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	78.3269	330	1980	95	below_threshold
Fontibacillus solani	strain=CECT 8693	GCA_014138385.1	1572857	1572857	type	True	78.2504	320	1980	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	78.1234	257	1980	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.802	109	1980	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.7257	224	1980	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.6418	215	1980	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.5924	210	1980	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	77.5073	113	1980	95	below_threshold
Paenibacillus turicensis	strain=DSM 14349	GCA_017873435.1	160487	160487	type	True	77.488	168	1980	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.3959	253	1980	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.3243	182	1980	95	below_threshold
Paenibacillus wulumuqiensis	strain=Y24	GCA_000971965.1	1567107	1567107	type	True	77.2671	55	1980	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:09,526] [INFO] DFAST Taxonomy check result was written to GCF_003994475.1_ASM399447v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:09,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:09,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:09,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference/checkm_data
[2024-01-24 11:27:09,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:09,593] [INFO] Task started: CheckM
[2024-01-24 11:27:09,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003994475.1_ASM399447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003994475.1_ASM399447v1_genomic.fna/checkm_input GCF_003994475.1_ASM399447v1_genomic.fna/checkm_result
[2024-01-24 11:27:53,146] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:53,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,173] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:53,174] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:53,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003994475.1_ASM399447v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:53,174] [INFO] Task started: Blastn
[2024-01-24 11:27:53,175] [INFO] Running command: blastn -query GCF_003994475.1_ASM399447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdafe5924-0bf0-4650-8300-1272ed0f06e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003994475.1_ASM399447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:53,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:53,970] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:53,970] [INFO] Target genome list was writen to GCF_003994475.1_ASM399447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:53,991] [INFO] Task started: fastANI
[2024-01-24 11:27:53,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg30dcda76-d180-44f0-ab56-7552a8995c4e/GCF_003994475.1_ASM399447v1_genomic.fna.gz --refList GCF_003994475.1_ASM399447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003994475.1_ASM399447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:17,277] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:17,300] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:17,301] [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_003994475.1	s__Paenibacillus_A anaericanus	100.0	1974	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014639155.1	s__Paenibacillus_A segetis	82.3186	1157	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001012825.1	s__Paenibacillus etheri	78.7605	205	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337355.1	s__Paenibacillus_A phaseoli	78.7187	279	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991425.1	s__Paenibacillus_A lutimineralis	78.6273	265	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102215.1	s__Paenibacillus_A panacisegetis	78.3422	328	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.17	97.17	0.85	0.85	2	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	78.0761	257	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	77.9755	219	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403325.1	s__Paenibacillus_A vini	77.9381	305	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCF_001682865.1	s__Paenibacillus_C sp001682865	77.8706	73	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.12	99.12	0.94	0.94	2	-
GCF_017086365.1	s__Paenibacillus sp017086365	77.802	109	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725205.1	s__Paenibacillus_A timonensis	77.6943	212	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
GCF_001685395.1	s__Paenibacillus_A yonginensis	77.6676	113	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	77.5366	212	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017873435.1	s__Paenibacillus_A turicensis	77.4825	167	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381905.1	s__Paenibacillus_A fonticola	77.3863	251	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919145.1	s__Paenibacillus_A sp018919145	77.3243	182	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971965.1	s__Paenibacillus_J wulumuqiensis	77.3108	55	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012912005.1	s__Paenibacillus sp012912005	77.1885	103	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333375.1	s__Paenibacillus cookii	77.0303	90	1980	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.09	99.09	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:17,302] [INFO] GTDB search result was written to GCF_003994475.1_ASM399447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:17,303] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:17,307] [INFO] DFAST_QC result json was written to GCF_003994475.1_ASM399447v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:17,307] [INFO] DFAST_QC completed!
[2024-01-24 11:28:17,307] [INFO] Total running time: 0h1m50s