[2024-01-24 14:19:00,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:00,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:00,852] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference
[2024-01-24 14:19:02,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:02,184] [INFO] Task started: Prodigal
[2024-01-24 14:19:02,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg761c9cfb-98da-4afe-b721-afe38a5142d9/GCF_002019735.1_ASM201973v1_genomic.fna.gz | prodigal -d GCF_002019735.1_ASM201973v1_genomic.fna/cds.fna -a GCF_002019735.1_ASM201973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:11,617] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:11,617] [INFO] Task started: HMMsearch
[2024-01-24 14:19:11,617] [INFO] Running command: hmmsearch --tblout GCF_002019735.1_ASM201973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference/reference_markers.hmm GCF_002019735.1_ASM201973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:11,924] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:11,925] [INFO] Found 6/6 markers.
[2024-01-24 14:19:11,964] [INFO] Query marker FASTA was written to GCF_002019735.1_ASM201973v1_genomic.fna/markers.fasta
[2024-01-24 14:19:11,964] [INFO] Task started: Blastn
[2024-01-24 14:19:11,964] [INFO] Running command: blastn -query GCF_002019735.1_ASM201973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference/reference_markers.fasta -out GCF_002019735.1_ASM201973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:12,590] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:12,594] [INFO] Selected 22 target genomes.
[2024-01-24 14:19:12,594] [INFO] Target genome list was writen to GCF_002019735.1_ASM201973v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:12,604] [INFO] Task started: fastANI
[2024-01-24 14:19:12,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg761c9cfb-98da-4afe-b721-afe38a5142d9/GCF_002019735.1_ASM201973v1_genomic.fna.gz --refList GCF_002019735.1_ASM201973v1_genomic.fna/target_genomes.txt --output GCF_002019735.1_ASM201973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:28,239] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:28,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:28,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:28,249] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:28,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:28,250] [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
Salipaludibacillus agaradhaerens	strain=DSM 8721	GCA_002019735.1	76935	76935	type	True	100.0	1439	1439	95	conclusive
Evansella clarkii	strain=DSM 8720	GCA_002019695.1	79879	79879	type	True	79.4624	85	1439	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	79.1335	62	1439	95	below_threshold
Salipaludibacillus keqinensis	strain=KQ-12	GCA_003226325.1	2045207	2045207	type	True	77.9662	162	1439	95	below_threshold
Salipaludibacillus neizhouensis	strain=DSM 19794	GCA_002886185.1	885475	885475	type	True	77.9632	138	1439	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	77.4467	61	1439	95	below_threshold
Salipaludibacillus neizhouensis	strain=KCTC 13187	GCA_003615245.1	885475	885475	type	True	77.0457	138	1439	95	below_threshold
Anaerobacillus alkalilacustris	strain=DSM 18345	GCA_001866005.1	393763	393763	type	True	77.013	64	1439	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.6813	52	1439	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	75.9696	54	1439	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	75.9696	54	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:28,251] [INFO] DFAST Taxonomy check result was written to GCF_002019735.1_ASM201973v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:28,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:28,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:28,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference/checkm_data
[2024-01-24 14:19:28,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:28,303] [INFO] Task started: CheckM
[2024-01-24 14:19:28,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019735.1_ASM201973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019735.1_ASM201973v1_genomic.fna/checkm_input GCF_002019735.1_ASM201973v1_genomic.fna/checkm_result
[2024-01-24 14:20:02,480] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:02,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,500] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:02,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:02,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019735.1_ASM201973v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:02,501] [INFO] Task started: Blastn
[2024-01-24 14:20:02,502] [INFO] Running command: blastn -query GCF_002019735.1_ASM201973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6b6d9d5-d580-4839-bdd6-e04518815f8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019735.1_ASM201973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:03,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:03,323] [INFO] Selected 24 target genomes.
[2024-01-24 14:20:03,323] [INFO] Target genome list was writen to GCF_002019735.1_ASM201973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:03,369] [INFO] Task started: fastANI
[2024-01-24 14:20:03,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg761c9cfb-98da-4afe-b721-afe38a5142d9/GCF_002019735.1_ASM201973v1_genomic.fna.gz --refList GCF_002019735.1_ASM201973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019735.1_ASM201973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:19,561] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:19,572] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:19,572] [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_002019735.1	s__Salipaludibacillus agaradhaerens	100.0	1438	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002019695.1	s__Evansella clarkii	79.4585	84	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Evansella	95.0	98.30	98.30	0.93	0.93	2	-
GCF_002886185.1	s__Salipaludibacillus neizhouensis	78.1518	140	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001244735.1	s__Bacillus_J andreraoultii	78.0946	50	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__DSM-16016;f__Caldibacillaceae;g__Bacillus_J	95.0	100.00	100.00	0.99	0.99	4	-
GCF_003226325.1	s__Salipaludibacillus keqinensis	77.9385	164	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salipaludibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	77.4416	62	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429705.1	s__Alteribacter aurantiacus	77.2986	64	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318295.1	s__Maribacillus taeanensis	76.6824	51	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513135.1	s__Bacillus_L akibai	75.9696	54	1439	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:19,574] [INFO] GTDB search result was written to GCF_002019735.1_ASM201973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:19,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:19,578] [INFO] DFAST_QC result json was written to GCF_002019735.1_ASM201973v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:19,578] [INFO] DFAST_QC completed!
[2024-01-24 14:20:19,578] [INFO] Total running time: 0h1m19s