[2024-01-24 14:28:02,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference
[2024-01-24 14:28:04,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,098] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf7a22b1-134f-4e69-95f9-5ebe384cd25e/GCF_021532315.1_ASM2153231v1_genomic.fna.gz | prodigal -d GCF_021532315.1_ASM2153231v1_genomic.fna/cds.fna -a GCF_021532315.1_ASM2153231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:17,067] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:17,067] [INFO] Task started: HMMsearch
[2024-01-24 14:28:17,067] [INFO] Running command: hmmsearch --tblout GCF_021532315.1_ASM2153231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference/reference_markers.hmm GCF_021532315.1_ASM2153231v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:17,443] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:17,444] [INFO] Found 6/6 markers.
[2024-01-24 14:28:17,489] [INFO] Query marker FASTA was written to GCF_021532315.1_ASM2153231v1_genomic.fna/markers.fasta
[2024-01-24 14:28:17,489] [INFO] Task started: Blastn
[2024-01-24 14:28:17,489] [INFO] Running command: blastn -query GCF_021532315.1_ASM2153231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference/reference_markers.fasta -out GCF_021532315.1_ASM2153231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:18,089] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:18,092] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:18,093] [INFO] Target genome list was writen to GCF_021532315.1_ASM2153231v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:18,120] [INFO] Task started: fastANI
[2024-01-24 14:28:18,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf7a22b1-134f-4e69-95f9-5ebe384cd25e/GCF_021532315.1_ASM2153231v1_genomic.fna.gz --refList GCF_021532315.1_ASM2153231v1_genomic.fna/target_genomes.txt --output GCF_021532315.1_ASM2153231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:37,107] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:37,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:37,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:37,121] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:37,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:37,122] [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 tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	100.0	1628	1629	95	conclusive
Paenibacillus sambharensis	strain=SMB1	GCA_003233845.1	1803190	1803190	type	True	87.3304	1409	1629	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.5769	172	1629	95	below_threshold
Paenibacillus pinihumi	strain=DSM 23905	GCA_000422505.1	669462	669462	type	True	77.3024	141	1629	95	below_threshold
Paenibacillus pinisoli	strain=JCM 19203	GCA_003605435.1	1276110	1276110	type	True	77.2679	146	1629	95	below_threshold
Paenibacillus daejeonensis	strain=DSM 15491	GCA_000378385.1	135193	135193	type	True	77.1236	126	1629	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	77.0305	122	1629	95	below_threshold
Paenibacillus abyssi	strain=CGMCC 1.12987	GCA_014640295.1	1340531	1340531	type	True	77.0232	184	1629	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	77.0189	74	1629	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.948	141	1629	95	below_threshold
Paenibacillus lycopersici	strain=12200R-189	GCA_010119935.1	2704462	2704462	type	True	76.892	148	1629	95	below_threshold
Paenibacillus taihuensis	strain=CGMCC 1.10966	GCA_003386535.1	1156355	1156355	type	True	76.8086	140	1629	95	below_threshold
Paenibacillus prosopidis	strain=CECT 7506	GCA_003337375.1	630520	630520	type	True	76.7911	110	1629	95	below_threshold
Paenibacillus methanolicus	strain=BL24	GCA_008124765.1	582686	582686	type	True	76.7505	161	1629	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.6196	103	1629	95	below_threshold
Paenibacillus yonginensis	strain=DCY84	GCA_001685395.1	1462996	1462996	type	True	76.4642	75	1629	95	below_threshold
Paenibacillus bovis	strain=BD3526	GCA_001421015.2	1616788	1616788	type	True	75.9431	70	1629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:37,124] [INFO] DFAST Taxonomy check result was written to GCF_021532315.1_ASM2153231v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:37,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:37,125] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:37,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference/checkm_data
[2024-01-24 14:28:37,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:37,175] [INFO] Task started: CheckM
[2024-01-24 14:28:37,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021532315.1_ASM2153231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021532315.1_ASM2153231v1_genomic.fna/checkm_input GCF_021532315.1_ASM2153231v1_genomic.fna/checkm_result
[2024-01-24 14:29:19,811] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:19,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:19,834] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:19,834] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:19,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021532315.1_ASM2153231v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:19,835] [INFO] Task started: Blastn
[2024-01-24 14:29:19,835] [INFO] Running command: blastn -query GCF_021532315.1_ASM2153231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e35ebec-e92e-46c6-925b-47b3300db5b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_021532315.1_ASM2153231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:20,644] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:20,653] [INFO] Selected 25 target genomes.
[2024-01-24 14:29:20,653] [INFO] Target genome list was writen to GCF_021532315.1_ASM2153231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:20,692] [INFO] Task started: fastANI
[2024-01-24 14:29:20,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf7a22b1-134f-4e69-95f9-5ebe384cd25e/GCF_021532315.1_ASM2153231v1_genomic.fna.gz --refList GCF_021532315.1_ASM2153231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021532315.1_ASM2153231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:45,286] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:45,313] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:29:45,313] [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_003233845.1	s__Paenibacillus_I sambharensis	87.3304	1409	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000598065.1	s__Paenibacillus_I darwinianus	77.5585	173	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_I	95.0	99.89	99.87	0.94	0.94	3	-
GCF_000422505.1	s__Paenibacillus_D pinihumi	77.3024	141	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	99.89	99.89	1.00	1.00	2	-
GCF_003605435.1	s__Paenibacillus_C pinisoli	77.2858	145	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952225.1	s__Paenibacillus_Z albus	77.044	123	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640295.1	s__Paenibacillus_D abyssi	77.0105	185	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119935.1	s__Paenibacillus_Z lycopersici	76.8919	148	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851045.1	s__Paenibacillus_D sp003851045	76.863	173	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422485.1	s__Paenibacillus_O pasadenensis	76.8529	127	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	99.23	98.68	0.94	0.90	4	-
GCF_003386535.1	s__Paenibacillus_Z taihuensis	76.822	141	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337375.1	s__Paenibacillus_C prosopidis	76.7911	110	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124765.1	s__Paenibacillus_Z methanolicus	76.7764	161	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112455.1	s__Paenibacillus_C agaridevorans	76.774	120	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	96.67	95.87	0.80	0.78	4	-
GCA_900105225.1	s__Paenibacillus_O sp900105225	76.7709	99	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614185.1	s__Paenibacillus_A aceti	76.7588	61	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004345425.1	s__Paenibacillus_C sp004345425	76.7531	153	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	99.19	99.19	0.96	0.96	2	-
GCF_014779765.1	s__Paenibacillus_T sp014779765	76.668	131	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_T	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110075.1	s__Paenibacillus_Z sp900110075	76.6475	115	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741035.1	s__Paenibacillus_C sp002741035	76.6342	134	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C	95.0	95.68	95.68	0.84	0.84	2	-
GCF_907165215.1	s__Thermobacillus xylanilyticus	76.6196	103	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus	95.0	97.85	97.19	0.88	0.86	4	-
GCF_003994465.1	s__Paenibacillus_A zeisoli	76.5364	59	1629	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_001685395.1	s__Paenibacillus_A yonginensis	76.4642	75	1629	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_018918005.1	s__MSJ-34 sp018918005	76.4442	73	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__MSJ-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900069005.2	s__Paenibacillus_A sp900069005	76.2169	70	1629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.72	99.44	0.97	0.94	3	-
GCF_001421015.2	s__Paenibacillus_J bovis	75.9147	68	1629	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 14:29:45,315] [INFO] GTDB search result was written to GCF_021532315.1_ASM2153231v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:45,316] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:45,320] [INFO] DFAST_QC result json was written to GCF_021532315.1_ASM2153231v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:45,320] [INFO] DFAST_QC completed!
[2024-01-24 14:29:45,320] [INFO] Total running time: 0h1m42s