[2024-01-25 20:06:50,618] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:06:50,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:06:50,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference
[2024-01-25 20:06:51,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:06:51,787] [INFO] Task started: Prodigal
[2024-01-25 20:06:51,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f538c4d-124f-4e91-9316-892a19722a19/GCF_014635365.1_ASM1463536v1_genomic.fna.gz | prodigal -d GCF_014635365.1_ASM1463536v1_genomic.fna/cds.fna -a GCF_014635365.1_ASM1463536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:06:54,832] [INFO] Task succeeded: Prodigal
[2024-01-25 20:06:54,832] [INFO] Task started: HMMsearch
[2024-01-25 20:06:54,832] [INFO] Running command: hmmsearch --tblout GCF_014635365.1_ASM1463536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference/reference_markers.hmm GCF_014635365.1_ASM1463536v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:06:55,027] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:06:55,028] [INFO] Found 6/6 markers.
[2024-01-25 20:06:55,056] [INFO] Query marker FASTA was written to GCF_014635365.1_ASM1463536v1_genomic.fna/markers.fasta
[2024-01-25 20:06:55,058] [INFO] Task started: Blastn
[2024-01-25 20:06:55,058] [INFO] Running command: blastn -query GCF_014635365.1_ASM1463536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference/reference_markers.fasta -out GCF_014635365.1_ASM1463536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:55,616] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:55,622] [INFO] Selected 20 target genomes.
[2024-01-25 20:06:55,622] [INFO] Target genome list was writen to GCF_014635365.1_ASM1463536v1_genomic.fna/target_genomes.txt
[2024-01-25 20:06:55,652] [INFO] Task started: fastANI
[2024-01-25 20:06:55,652] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f538c4d-124f-4e91-9316-892a19722a19/GCF_014635365.1_ASM1463536v1_genomic.fna.gz --refList GCF_014635365.1_ASM1463536v1_genomic.fna/target_genomes.txt --output GCF_014635365.1_ASM1463536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:01,733] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:01,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:01,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:01,745] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:07:01,745] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:01,746] [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 apis	strain=CCM 8403	GCA_014635365.1	303541	303541	type	True	100.0	556	558	95	conclusive
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	99.9507	492	558	95	conclusive
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	79.7548	231	558	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	79.5577	217	558	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	78.6573	127	558	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	78.6228	125	558	95	below_threshold
Lactobacillus acidophilus	strain=CIP 76.13	GCA_000469705.1	1579	1579	type	True	78.6037	114	558	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	78.548	118	558	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_003047065.1	1579	1579	type	True	78.5239	117	558	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	78.5224	113	558	95	below_threshold
Lactobacillus acetotolerans	strain=JCM 3825	GCA_014648715.1	1600	1600	type	True	78.5009	133	558	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	78.5001	125	558	95	below_threshold
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	78.4892	126	558	95	below_threshold
Lactobacillus acetotolerans	strain=DSM 20749	GCA_001436775.1	1600	1600	type	True	78.4464	133	558	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	78.4125	117	558	95	below_threshold
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	78.4032	127	558	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	78.3298	117	558	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	78.2716	107	558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:01,747] [INFO] DFAST Taxonomy check result was written to GCF_014635365.1_ASM1463536v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:01,747] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:01,747] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:01,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference/checkm_data
[2024-01-25 20:07:01,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:01,768] [INFO] Task started: CheckM
[2024-01-25 20:07:01,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635365.1_ASM1463536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635365.1_ASM1463536v1_genomic.fna/checkm_input GCF_014635365.1_ASM1463536v1_genomic.fna/checkm_result
[2024-01-25 20:07:17,157] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:17,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:17,173] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:17,173] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:17,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635365.1_ASM1463536v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:17,173] [INFO] Task started: Blastn
[2024-01-25 20:07:17,173] [INFO] Running command: blastn -query GCF_014635365.1_ASM1463536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e985431-f140-44af-8892-57191cfd5ca9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635365.1_ASM1463536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:17,935] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:17,938] [INFO] Selected 19 target genomes.
[2024-01-25 20:07:17,938] [INFO] Target genome list was writen to GCF_014635365.1_ASM1463536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:17,969] [INFO] Task started: fastANI
[2024-01-25 20:07:17,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f538c4d-124f-4e91-9316-892a19722a19/GCF_014635365.1_ASM1463536v1_genomic.fna.gz --refList GCF_014635365.1_ASM1463536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635365.1_ASM1463536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:24,361] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:24,372] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:24,372] [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_002837055.1	s__Lactobacillus apis	99.9507	492	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.63	96.48	0.93	0.86	10	conclusive
GCF_002916935.1	s__Lactobacillus panisapium	80.2395	267	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346935.1	s__Lactobacillus melliventris	79.7034	223	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
GCF_000970755.1	s__Lactobacillus kimbladii_A	79.6528	226	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	79.4602	229	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967195.1	s__Lactobacillus kullabergensis	79.4478	237	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.65	96.49	0.90	0.88	4	-
GCF_016100975.1	s__Lactobacillus sp016100975	79.3662	237	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000760615.1	s__Lactobacillus sp000760615	79.3394	247	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.94	96.94	0.89	0.89	2	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	79.258	219	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
GCA_014803915.1	s__Lactobacillus sp014803915	78.836	90	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615285.1	s__Lactobacillus kitasatonis	78.6742	125	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001591845.1	s__Lactobacillus acidophilus	78.4086	114	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_018987235.1	s__Lactobacillus crispatus	78.349	131	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_001436305.1	s__Lactobacillus ultunensis	78.2716	107	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_000159355.1	s__Lactobacillus johnsonii	78.0798	86	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCA_002418055.1	s__Lactobacillus sp002418055	77.6248	52	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.84	99.82	0.90	0.90	3	-
GCF_000425905.1	s__Lactobacillus psittaci	77.5924	99	558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:24,374] [INFO] GTDB search result was written to GCF_014635365.1_ASM1463536v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:24,374] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:24,378] [INFO] DFAST_QC result json was written to GCF_014635365.1_ASM1463536v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:24,378] [INFO] DFAST_QC completed!
[2024-01-25 20:07:24,378] [INFO] Total running time: 0h0m34s