[2024-01-25 19:43:20,456] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:20,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:20,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference
[2024-01-25 19:43:21,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:21,615] [INFO] Task started: Prodigal
[2024-01-25 19:43:21,615] [INFO] Running command: gunzip -c /var/lib/cwl/stge1b6514f-0989-49de-a9b7-de02b66aea1b/GCF_000520735.1_s9_genomic.fna.gz | prodigal -d GCF_000520735.1_s9_genomic.fna/cds.fna -a GCF_000520735.1_s9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:32,215] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:32,215] [INFO] Task started: HMMsearch
[2024-01-25 19:43:32,215] [INFO] Running command: hmmsearch --tblout GCF_000520735.1_s9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference/reference_markers.hmm GCF_000520735.1_s9_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:32,468] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:32,471] [INFO] Found 6/6 markers.
[2024-01-25 19:43:32,510] [INFO] Query marker FASTA was written to GCF_000520735.1_s9_genomic.fna/markers.fasta
[2024-01-25 19:43:32,511] [INFO] Task started: Blastn
[2024-01-25 19:43:32,511] [INFO] Running command: blastn -query GCF_000520735.1_s9_genomic.fna/markers.fasta -db /var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference/reference_markers.fasta -out GCF_000520735.1_s9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:33,082] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:33,085] [INFO] Selected 13 target genomes.
[2024-01-25 19:43:33,086] [INFO] Target genome list was writen to GCF_000520735.1_s9_genomic.fna/target_genomes.txt
[2024-01-25 19:43:33,091] [INFO] Task started: fastANI
[2024-01-25 19:43:33,091] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b6514f-0989-49de-a9b7-de02b66aea1b/GCF_000520735.1_s9_genomic.fna.gz --refList GCF_000520735.1_s9_genomic.fna/target_genomes.txt --output GCF_000520735.1_s9_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:48,337] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:48,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:48,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:48,347] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:43:48,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:48,347] [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 forsythiae	strain=T98	GCA_000520735.1	365616	365616	type	True	100.0	1300	1320	95	conclusive
Paenibacillus sophorae	strain=DSM 23020	GCA_018966525.1	1333845	1333845	type	True	87.7133	1042	1320	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	87.6785	1055	1320	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	87.2327	842	1320	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	84.6443	922	1320	95	below_threshold
Paenibacillus apii	strain=7124	GCA_011043685.1	1850370	1850370	type	True	84.3451	934	1320	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	84.2708	916	1320	95	below_threshold
Paenibacillus stellifer	strain=DSM 14472	GCA_000758685.1	169760	169760	type	True	80.3148	558	1320	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	79.9491	557	1320	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	78.3048	363	1320	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	78.2766	343	1320	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.8898	190	1320	95	below_threshold
Paenibacillus hemerocallicola	strain=KCTC 33185	GCA_006265175.1	1172614	1172614	type	True	75.9808	97	1320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:48,354] [INFO] DFAST Taxonomy check result was written to GCF_000520735.1_s9_genomic.fna/tc_result.tsv
[2024-01-25 19:43:48,354] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:48,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:48,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference/checkm_data
[2024-01-25 19:43:48,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:48,409] [INFO] Task started: CheckM
[2024-01-25 19:43:48,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000520735.1_s9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000520735.1_s9_genomic.fna/checkm_input GCF_000520735.1_s9_genomic.fna/checkm_result
[2024-01-25 19:44:23,870] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:23,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:23,889] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:23,889] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:23,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000520735.1_s9_genomic.fna/markers.fasta)
[2024-01-25 19:44:23,890] [INFO] Task started: Blastn
[2024-01-25 19:44:23,890] [INFO] Running command: blastn -query GCF_000520735.1_s9_genomic.fna/markers.fasta -db /var/lib/cwl/stg53f65cd9-8e06-462c-9c34-77b030d30b28/dqc_reference/reference_markers_gtdb.fasta -out GCF_000520735.1_s9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:24,689] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:24,692] [INFO] Selected 10 target genomes.
[2024-01-25 19:44:24,692] [INFO] Target genome list was writen to GCF_000520735.1_s9_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:24,702] [INFO] Task started: fastANI
[2024-01-25 19:44:24,702] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b6514f-0989-49de-a9b7-de02b66aea1b/GCF_000520735.1_s9_genomic.fna.gz --refList GCF_000520735.1_s9_genomic.fna/target_genomes_gtdb.txt --output GCF_000520735.1_s9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:35,926] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:35,933] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:35,933] [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_000520735.1	s__Paenibacillus forsythiae	100.0	1300	1320	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_018966525.1	s__Paenibacillus sophorae	87.708	1043	1320	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	87.553	1049	1320	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	87.3113	1015	1320	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000520715.1	s__Paenibacillus zanthoxyli	87.2489	840	1320	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854965.1	s__Paenibacillus sp003854965	84.6417	922	1320	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_000612505.1	s__Paenibacillus sabinae	84.2708	916	1320	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.70	95.69	0.89	0.89	3	-
GCF_000758685.1	s__Paenibacillus stellifer	80.3109	558	1320	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	78.7463	362	1320	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265175.1	s__Paenibacillus_AB hemerocallicola	75.9808	97	1320	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:35,935] [INFO] GTDB search result was written to GCF_000520735.1_s9_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:35,935] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:35,941] [INFO] DFAST_QC result json was written to GCF_000520735.1_s9_genomic.fna/dqc_result.json
[2024-01-25 19:44:35,941] [INFO] DFAST_QC completed!
[2024-01-25 19:44:35,941] [INFO] Total running time: 0h1m15s