[2024-01-24 12:53:54,865] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:54,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:54,868] [INFO] DQC Reference Directory: /var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference
[2024-01-24 12:53:56,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,124] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,125] [INFO] Running command: gunzip -c /var/lib/cwl/stg30284ed1-7f71-4c28-83e3-4032ba62cb6d/GCF_000296835.1_ASM29683v1_genomic.fna.gz | prodigal -d GCF_000296835.1_ASM29683v1_genomic.fna/cds.fna -a GCF_000296835.1_ASM29683v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:59,745] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:59,746] [INFO] Task started: HMMsearch
[2024-01-24 12:53:59,746] [INFO] Running command: hmmsearch --tblout GCF_000296835.1_ASM29683v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference/reference_markers.hmm GCF_000296835.1_ASM29683v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:59,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:59,961] [INFO] Found 6/6 markers.
[2024-01-24 12:53:59,982] [INFO] Query marker FASTA was written to GCF_000296835.1_ASM29683v1_genomic.fna/markers.fasta
[2024-01-24 12:53:59,982] [INFO] Task started: Blastn
[2024-01-24 12:53:59,982] [INFO] Running command: blastn -query GCF_000296835.1_ASM29683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference/reference_markers.fasta -out GCF_000296835.1_ASM29683v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:00,650] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:00,654] [INFO] Selected 17 target genomes.
[2024-01-24 12:54:00,654] [INFO] Target genome list was writen to GCF_000296835.1_ASM29683v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:00,679] [INFO] Task started: fastANI
[2024-01-24 12:54:00,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg30284ed1-7f71-4c28-83e3-4032ba62cb6d/GCF_000296835.1_ASM29683v1_genomic.fna.gz --refList GCF_000296835.1_ASM29683v1_genomic.fna/target_genomes.txt --output GCF_000296835.1_ASM29683v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:06,948] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:06,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:06,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:06,963] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:06,963] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:06,963] [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
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	100.0	627	627	95	conclusive
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	99.973	610	627	95	conclusive
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	81.5559	260	627	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	81.5394	253	627	95	below_threshold
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	81.4701	260	627	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	81.3947	248	627	95	below_threshold
Lactobacillus taiwanensis	strain=DSM 21401	GCA_001436695.1	508451	508451	type	True	81.1708	251	627	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_000159355.1	33959	33959	type	True	80.1196	242	627	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_001433975.1	33959	33959	type	True	79.9695	236	627	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.954	188	627	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_003423665.1	947835	947835	type	True	79.9041	186	627	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.7842	162	627	95	below_threshold
Lactobacillus colini	strain=DSM 101872	GCA_017874575.1	1819254	1819254	type	True	79.4185	181	627	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	78.7343	146	627	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.0417	89	627	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	77.8033	59	627	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:06,966] [INFO] DFAST Taxonomy check result was written to GCF_000296835.1_ASM29683v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:06,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:06,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:06,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference/checkm_data
[2024-01-24 12:54:06,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:06,997] [INFO] Task started: CheckM
[2024-01-24 12:54:06,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000296835.1_ASM29683v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000296835.1_ASM29683v1_genomic.fna/checkm_input GCF_000296835.1_ASM29683v1_genomic.fna/checkm_result
[2024-01-24 12:54:25,455] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:25,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:25,481] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:25,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:25,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000296835.1_ASM29683v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:25,482] [INFO] Task started: Blastn
[2024-01-24 12:54:25,482] [INFO] Running command: blastn -query GCF_000296835.1_ASM29683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb22ddae0-a6bd-4f1b-beb5-600903e0c925/dqc_reference/reference_markers_gtdb.fasta -out GCF_000296835.1_ASM29683v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:26,320] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:26,323] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:26,324] [INFO] Target genome list was writen to GCF_000296835.1_ASM29683v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:26,334] [INFO] Task started: fastANI
[2024-01-24 12:54:26,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg30284ed1-7f71-4c28-83e3-4032ba62cb6d/GCF_000296835.1_ASM29683v1_genomic.fna.gz --refList GCF_000296835.1_ASM29683v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000296835.1_ASM29683v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:31,337] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:31,350] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:31,350] [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_000296835.1	s__Lactobacillus hominis	100.0	627	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	conclusive
GCF_000014425.1	s__Lactobacillus gasseri	81.5394	253	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_003584685.1	s__Lactobacillus paragasseri	81.3774	264	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_001436695.1	s__Lactobacillus taiwanensis	81.1797	250	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCA_910589175.1	s__Lactobacillus sp910589175	80.5819	226	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159355.1	s__Lactobacillus johnsonii	80.1427	241	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCA_910589675.1	s__Lactobacillus sp910589675	79.9765	190	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_003423665.1	s__Lactobacillus rodentium	79.9041	186	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803895.1	s__Lactobacillus sp014803895	79.7368	183	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874575.1	s__Lactobacillus colini	79.4221	182	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018987235.1	s__Lactobacillus crispatus	79.1788	175	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	78.7692	145	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_000425905.1	s__Lactobacillus psittaci	78.339	115	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_900112665.1	s__Lactobacillus bombicola	77.1922	75	627	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.76	97.11	0.90	0.87	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:31,352] [INFO] GTDB search result was written to GCF_000296835.1_ASM29683v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:31,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:31,357] [INFO] DFAST_QC result json was written to GCF_000296835.1_ASM29683v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:31,357] [INFO] DFAST_QC completed!
[2024-01-24 12:54:31,357] [INFO] Total running time: 0h0m36s