[2024-01-25 17:34:07,120] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,124] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference
[2024-01-25 17:34:08,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,955] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgd159da81-6a0a-45ed-a2d7-652d40e6a8c2/GCF_001434435.1_ASM143443v1_genomic.fna.gz | prodigal -d GCF_001434435.1_ASM143443v1_genomic.fna/cds.fna -a GCF_001434435.1_ASM143443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:12,568] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:12,568] [INFO] Task started: HMMsearch
[2024-01-25 17:34:12,568] [INFO] Running command: hmmsearch --tblout GCF_001434435.1_ASM143443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference/reference_markers.hmm GCF_001434435.1_ASM143443v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:12,834] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:12,835] [INFO] Found 6/6 markers.
[2024-01-25 17:34:12,875] [INFO] Query marker FASTA was written to GCF_001434435.1_ASM143443v1_genomic.fna/markers.fasta
[2024-01-25 17:34:12,876] [INFO] Task started: Blastn
[2024-01-25 17:34:12,876] [INFO] Running command: blastn -query GCF_001434435.1_ASM143443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference/reference_markers.fasta -out GCF_001434435.1_ASM143443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:14,076] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:14,079] [INFO] Selected 13 target genomes.
[2024-01-25 17:34:14,080] [INFO] Target genome list was writen to GCF_001434435.1_ASM143443v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:14,150] [INFO] Task started: fastANI
[2024-01-25 17:34:14,150] [INFO] Running command: fastANI --query /var/lib/cwl/stgd159da81-6a0a-45ed-a2d7-652d40e6a8c2/GCF_001434435.1_ASM143443v1_genomic.fna.gz --refList GCF_001434435.1_ASM143443v1_genomic.fna/target_genomes.txt --output GCF_001434435.1_ASM143443v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:19,925] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:19,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:19,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:19,933] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:19,933] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:19,933] [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 kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	100.0	622	624	95	conclusive
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	99.9714	613	624	95	conclusive
Lactobacillus amylovorus	strain=DSM 20531	GCA_001433985.1	1604	1604	type	True	92.6812	489	624	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	92.3877	530	624	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	85.38	407	624	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	83.5928	397	624	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	83.2451	422	624	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	83.2445	322	624	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	78.1016	90	624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:19,934] [INFO] DFAST Taxonomy check result was written to GCF_001434435.1_ASM143443v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:19,935] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:19,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:19,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference/checkm_data
[2024-01-25 17:34:19,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:19,962] [INFO] Task started: CheckM
[2024-01-25 17:34:19,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001434435.1_ASM143443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001434435.1_ASM143443v1_genomic.fna/checkm_input GCF_001434435.1_ASM143443v1_genomic.fna/checkm_result
[2024-01-25 17:34:36,765] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:36,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:36,780] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:36,780] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:36,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001434435.1_ASM143443v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:36,781] [INFO] Task started: Blastn
[2024-01-25 17:34:36,781] [INFO] Running command: blastn -query GCF_001434435.1_ASM143443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1aaa809-8185-46bb-b996-124171386d70/dqc_reference/reference_markers_gtdb.fasta -out GCF_001434435.1_ASM143443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:37,658] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:37,663] [INFO] Selected 9 target genomes.
[2024-01-25 17:34:37,663] [INFO] Target genome list was writen to GCF_001434435.1_ASM143443v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:34:37,672] [INFO] Task started: fastANI
[2024-01-25 17:34:37,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgd159da81-6a0a-45ed-a2d7-652d40e6a8c2/GCF_001434435.1_ASM143443v1_genomic.fna.gz --refList GCF_001434435.1_ASM143443v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001434435.1_ASM143443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:34:42,033] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:42,039] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:34:42,039] [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_000615285.1	s__Lactobacillus kitasatonis	99.9714	613	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	conclusive
GCF_002706375.1	s__Lactobacillus amylovorus	92.4412	529	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001434975.1	s__Lactobacillus gallinarum	85.38	407	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001436305.1	s__Lactobacillus ultunensis	83.5928	397	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_001591845.1	s__Lactobacillus acidophilus	83.2916	416	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000160855.1	s__Lactobacillus helveticus	83.2837	365	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_018987235.1	s__Lactobacillus crispatus	82.6631	371	624	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	82.2364	356	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_004009905.1	s__Lactobacillus xujianguonis	80.8107	247	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:34:42,041] [INFO] GTDB search result was written to GCF_001434435.1_ASM143443v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:34:42,041] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:34:42,044] [INFO] DFAST_QC result json was written to GCF_001434435.1_ASM143443v1_genomic.fna/dqc_result.json
[2024-01-25 17:34:42,044] [INFO] DFAST_QC completed!
[2024-01-25 17:34:42,044] [INFO] Total running time: 0h0m35s