[2024-01-24 15:18:18,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,368] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference
[2024-01-24 15:18:19,612] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:19,613] [INFO] Task started: Prodigal
[2024-01-24 15:18:19,613] [INFO] Running command: gunzip -c /var/lib/cwl/stgf948991a-d32f-49b5-910c-a1fb948d7d9b/GCF_003931855.1_ASM393185v1_genomic.fna.gz | prodigal -d GCF_003931855.1_ASM393185v1_genomic.fna/cds.fna -a GCF_003931855.1_ASM393185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:34,247] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:34,248] [INFO] Task started: HMMsearch
[2024-01-24 15:18:34,248] [INFO] Running command: hmmsearch --tblout GCF_003931855.1_ASM393185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference/reference_markers.hmm GCF_003931855.1_ASM393185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:34,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:34,570] [INFO] Found 6/6 markers.
[2024-01-24 15:18:34,618] [INFO] Query marker FASTA was written to GCF_003931855.1_ASM393185v1_genomic.fna/markers.fasta
[2024-01-24 15:18:34,619] [INFO] Task started: Blastn
[2024-01-24 15:18:34,619] [INFO] Running command: blastn -query GCF_003931855.1_ASM393185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference/reference_markers.fasta -out GCF_003931855.1_ASM393185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:35,261] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:35,326] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:35,327] [INFO] Target genome list was writen to GCF_003931855.1_ASM393185v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:35,412] [INFO] Task started: fastANI
[2024-01-24 15:18:35,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgf948991a-d32f-49b5-910c-a1fb948d7d9b/GCF_003931855.1_ASM393185v1_genomic.fna.gz --refList GCF_003931855.1_ASM393185v1_genomic.fna/target_genomes.txt --output GCF_003931855.1_ASM393185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:52,135] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:52,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:52,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:52,148] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:52,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:52,148] [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 lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	100.0	1762	1762	95	conclusive
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	86.9386	1332	1762	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	82.0527	1080	1762	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	81.7201	957	1762	95	below_threshold
Paenibacillus oralis	strain=KCOM 3021	GCA_003863965.1	2490856	2490856	type	True	78.4916	321	1762	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	78.3274	130	1762	95	below_threshold
Fontibacillus solani	strain=CECT 8693	GCA_014138385.1	1572857	1572857	type	True	78.1326	272	1762	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.8935	128	1762	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.8743	292	1762	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.75	237	1762	95	below_threshold
Paenibacillus barengoltzii	strain=NBRC 101215	GCA_004000745.1	343517	343517	type	True	77.6918	253	1762	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.4316	221	1762	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	77.366	154	1762	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:52,151] [INFO] DFAST Taxonomy check result was written to GCF_003931855.1_ASM393185v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:52,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:52,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:52,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference/checkm_data
[2024-01-24 15:18:52,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:52,212] [INFO] Task started: CheckM
[2024-01-24 15:18:52,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003931855.1_ASM393185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003931855.1_ASM393185v1_genomic.fna/checkm_input GCF_003931855.1_ASM393185v1_genomic.fna/checkm_result
[2024-01-24 15:19:39,567] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:39,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:39,588] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:39,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:39,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003931855.1_ASM393185v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:39,588] [INFO] Task started: Blastn
[2024-01-24 15:19:39,588] [INFO] Running command: blastn -query GCF_003931855.1_ASM393185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf282151-b7d6-408d-9ba3-8e09afd8a71d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003931855.1_ASM393185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:40,376] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:40,380] [INFO] Selected 6 target genomes.
[2024-01-24 15:19:40,380] [INFO] Target genome list was writen to GCF_003931855.1_ASM393185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:40,387] [INFO] Task started: fastANI
[2024-01-24 15:19:40,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgf948991a-d32f-49b5-910c-a1fb948d7d9b/GCF_003931855.1_ASM393185v1_genomic.fna.gz --refList GCF_003931855.1_ASM393185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003931855.1_ASM393185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:49,071] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:49,085] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:49,086] [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_003931855.1	s__Paenibacillus_A lentus	100.0	1762	1762	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_900155685.1	s__Paenibacillus_A bouchesdurhonensis	86.9353	1333	1762	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_009725165.1	s__Paenibacillus_A woosongensis	82.653	1138	1762	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	95.99	95.99	0.91	0.91	2	-
GCF_001403875.1	s__Paenibacillus_A ihumii	82.0473	1081	1762	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_000381905.1	s__Paenibacillus_A fonticola	81.7147	959	1762	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_004000745.1	s__Paenibacillus_A barengoltzii	77.6789	254	1762	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.39	97.66	0.91	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:49,095] [INFO] GTDB search result was written to GCF_003931855.1_ASM393185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:49,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:49,100] [INFO] DFAST_QC result json was written to GCF_003931855.1_ASM393185v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:49,100] [INFO] DFAST_QC completed!
[2024-01-24 15:19:49,101] [INFO] Total running time: 0h1m31s