[2024-01-25 19:59:35,879] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:35,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:35,881] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference
[2024-01-25 19:59:37,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:37,016] [INFO] Task started: Prodigal
[2024-01-25 19:59:37,016] [INFO] Running command: gunzip -c /var/lib/cwl/stgb259990b-c4db-4d2c-802c-46c9885478a9/GCF_000758685.1_ASM75868v1_genomic.fna.gz | prodigal -d GCF_000758685.1_ASM75868v1_genomic.fna/cds.fna -a GCF_000758685.1_ASM75868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:50,397] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:50,397] [INFO] Task started: HMMsearch
[2024-01-25 19:59:50,397] [INFO] Running command: hmmsearch --tblout GCF_000758685.1_ASM75868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference/reference_markers.hmm GCF_000758685.1_ASM75868v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:50,659] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:50,660] [INFO] Found 6/6 markers.
[2024-01-25 19:59:50,704] [INFO] Query marker FASTA was written to GCF_000758685.1_ASM75868v1_genomic.fna/markers.fasta
[2024-01-25 19:59:50,704] [INFO] Task started: Blastn
[2024-01-25 19:59:50,704] [INFO] Running command: blastn -query GCF_000758685.1_ASM75868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference/reference_markers.fasta -out GCF_000758685.1_ASM75868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:51,284] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:51,286] [INFO] Selected 12 target genomes.
[2024-01-25 19:59:51,287] [INFO] Target genome list was writen to GCF_000758685.1_ASM75868v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:51,292] [INFO] Task started: fastANI
[2024-01-25 19:59:51,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgb259990b-c4db-4d2c-802c-46c9885478a9/GCF_000758685.1_ASM75868v1_genomic.fna.gz --refList GCF_000758685.1_ASM75868v1_genomic.fna/target_genomes.txt --output GCF_000758685.1_ASM75868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:04,491] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:04,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:04,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:04,500] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:04,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:04,500] [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 stellifer	strain=DSM 14472	GCA_000758685.1	169760	169760	type	True	100.0	1886	1886	95	conclusive
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	91.2685	1535	1886	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	80.605	752	1886	95	below_threshold
Paenibacillus sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	80.3299	727	1886	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	80.3043	752	1886	95	below_threshold
Paenibacillus apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	80.1918	766	1886	95	below_threshold
Paenibacillus forsythiae	strain=T98	GCA_000520735.1	365616	365616	type	True	80.0893	573	1886	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	80.0342	731	1886	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	79.9164	572	1886	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	78.7164	504	1886	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.8611	112	1886	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.3722	255	1886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:04,501] [INFO] DFAST Taxonomy check result was written to GCF_000758685.1_ASM75868v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:04,501] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:04,502] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:04,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference/checkm_data
[2024-01-25 20:00:04,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:04,556] [INFO] Task started: CheckM
[2024-01-25 20:00:04,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000758685.1_ASM75868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000758685.1_ASM75868v1_genomic.fna/checkm_input GCF_000758685.1_ASM75868v1_genomic.fna/checkm_result
[2024-01-25 20:00:45,490] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:45,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:00:45,509] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:45,510] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:45,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000758685.1_ASM75868v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:45,510] [INFO] Task started: Blastn
[2024-01-25 20:00:45,510] [INFO] Running command: blastn -query GCF_000758685.1_ASM75868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5dda7d4-82a3-436a-9654-b6be61d105fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000758685.1_ASM75868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:46,334] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:46,337] [INFO] Selected 10 target genomes.
[2024-01-25 20:00:46,337] [INFO] Target genome list was writen to GCF_000758685.1_ASM75868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:46,346] [INFO] Task started: fastANI
[2024-01-25 20:00:46,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgb259990b-c4db-4d2c-802c-46c9885478a9/GCF_000758685.1_ASM75868v1_genomic.fna.gz --refList GCF_000758685.1_ASM75868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000758685.1_ASM75868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:57,844] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:57,851] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:57,851] [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_000758685.1	s__Paenibacillus stellifer	100.0	1886	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000612505.1	s__Paenibacillus sabinae	80.5915	751	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.70	95.69	0.89	0.89	3	-
GCF_018966525.1	s__Paenibacillus sophorae	80.3343	728	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000756615.1	s__Paenibacillus durus	80.3206	739	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000993825.1	s__Paenibacillus durus_B	80.3166	731	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003854965.1	s__Paenibacillus sp003854965	80.3042	752	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_000520735.1	s__Paenibacillus forsythiae	80.1149	570	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000520715.1	s__Paenibacillus zanthoxyli	79.9048	574	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710135.1	s__Paenibacillus spiritus	78.9849	502	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099765.1	s__Paenibacillus typhae	78.1126	483	1886	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.38	98.38	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:57,852] [INFO] GTDB search result was written to GCF_000758685.1_ASM75868v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:57,853] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:57,855] [INFO] DFAST_QC result json was written to GCF_000758685.1_ASM75868v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:57,855] [INFO] DFAST_QC completed!
[2024-01-25 20:00:57,855] [INFO] Total running time: 0h1m22s