[2024-01-24 13:22:41,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:41,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:41,002] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference
[2024-01-24 13:22:42,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:42,307] [INFO] Task started: Prodigal
[2024-01-24 13:22:42,308] [INFO] Running command: gunzip -c /var/lib/cwl/stgeee714ce-d18e-483c-aea5-defbab187d4f/GCF_004000945.1_ASM400094v1_genomic.fna.gz | prodigal -d GCF_004000945.1_ASM400094v1_genomic.fna/cds.fna -a GCF_004000945.1_ASM400094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:02,796] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:02,796] [INFO] Task started: HMMsearch
[2024-01-24 13:23:02,796] [INFO] Running command: hmmsearch --tblout GCF_004000945.1_ASM400094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference/reference_markers.hmm GCF_004000945.1_ASM400094v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:03,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:03,091] [INFO] Found 6/6 markers.
[2024-01-24 13:23:03,153] [INFO] Query marker FASTA was written to GCF_004000945.1_ASM400094v1_genomic.fna/markers.fasta
[2024-01-24 13:23:03,153] [INFO] Task started: Blastn
[2024-01-24 13:23:03,153] [INFO] Running command: blastn -query GCF_004000945.1_ASM400094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference/reference_markers.fasta -out GCF_004000945.1_ASM400094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:03,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:03,746] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:03,746] [INFO] Target genome list was writen to GCF_004000945.1_ASM400094v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:03,753] [INFO] Task started: fastANI
[2024-01-24 13:23:03,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgeee714ce-d18e-483c-aea5-defbab187d4f/GCF_004000945.1_ASM400094v1_genomic.fna.gz --refList GCF_004000945.1_ASM400094v1_genomic.fna/target_genomes.txt --output GCF_004000945.1_ASM400094v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:21,170] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:21,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:21,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:21,183] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:21,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:21,184] [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 lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	100.0	2324	2327	95	conclusive
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	84.998	1499	2327	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	84.248	1352	2327	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	81.0596	1127	2327	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	80.7847	1088	2327	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	78.7788	377	2327	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	77.3998	201	2327	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.13	176	2327	95	below_threshold
Paenibacillus zanthoxyli	strain=JH29	GCA_000520715.1	369399	369399	type	True	77.0375	169	2327	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.8635	171	2327	95	below_threshold
Paenibacillus thalictri	strain=N2SHLJ1	GCA_004307995.1	2527873	2527873	type	True	76.8351	110	2327	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.5561	212	2327	95	below_threshold
Paenibacillus rhizovicinus	strain=14171R-81	GCA_010365285.1	2704463	2704463	type	True	76.3486	113	2327	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.318	100	2327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:21,222] [INFO] DFAST Taxonomy check result was written to GCF_004000945.1_ASM400094v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:21,222] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:21,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:21,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference/checkm_data
[2024-01-24 13:23:21,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:21,289] [INFO] Task started: CheckM
[2024-01-24 13:23:21,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004000945.1_ASM400094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004000945.1_ASM400094v1_genomic.fna/checkm_input GCF_004000945.1_ASM400094v1_genomic.fna/checkm_result
[2024-01-24 13:24:19,044] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:19,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:19,065] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:19,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:19,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004000945.1_ASM400094v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:19,066] [INFO] Task started: Blastn
[2024-01-24 13:24:19,066] [INFO] Running command: blastn -query GCF_004000945.1_ASM400094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9a23ab5-e199-487c-b766-a8792a1ded92/dqc_reference/reference_markers_gtdb.fasta -out GCF_004000945.1_ASM400094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:19,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:19,847] [INFO] Selected 6 target genomes.
[2024-01-24 13:24:19,847] [INFO] Target genome list was writen to GCF_004000945.1_ASM400094v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:19,856] [INFO] Task started: fastANI
[2024-01-24 13:24:19,856] [INFO] Running command: fastANI --query /var/lib/cwl/stgeee714ce-d18e-483c-aea5-defbab187d4f/GCF_004000945.1_ASM400094v1_genomic.fna.gz --refList GCF_004000945.1_ASM400094v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004000945.1_ASM400094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:30,398] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:30,405] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:30,406] [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_004000945.1	s__Paenibacillus lautus	100.0	2324	2327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.53	96.53	0.89	0.89	2	conclusive
GCF_002573715.1	s__Paenibacillus sp002573715	92.8573	1901	2327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.81	0.89	0.84	4	-
GCF_015326965.1	s__Paenibacillus sp001860525	92.2927	1972	2327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.48	95.93	0.88	0.85	4	-
GCF_014863545.1	s__Paenibacillus lautus_A	88.8189	1885	2327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.37	95.82	0.93	0.90	10	-
GCF_004000885.1	s__Paenibacillus glucanolyticus	84.998	1499	2327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.37	98.87	0.95	0.92	9	-
GCF_001277345.1	s__Paenibacillus solani	84.2409	1353	2327	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.74	96.74	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:30,407] [INFO] GTDB search result was written to GCF_004000945.1_ASM400094v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:30,408] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:30,411] [INFO] DFAST_QC result json was written to GCF_004000945.1_ASM400094v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:30,412] [INFO] DFAST_QC completed!
[2024-01-24 13:24:30,412] [INFO] Total running time: 0h1m49s