[2023-06-17 08:06:32,297] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:06:32,301] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:06:32,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference
[2023-06-17 08:06:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:06:33,649] [INFO] Task started: Prodigal
[2023-06-17 08:06:33,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg70c3bc45-d025-4e27-b9c2-290b51eb382c/GCA_003539685.1_ASM353968v1_genomic.fna.gz | prodigal -d GCA_003539685.1_ASM353968v1_genomic.fna/cds.fna -a GCA_003539685.1_ASM353968v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:06:35,768] [INFO] Task succeeded: Prodigal
[2023-06-17 08:06:35,769] [INFO] Task started: HMMsearch
[2023-06-17 08:06:35,769] [INFO] Running command: hmmsearch --tblout GCA_003539685.1_ASM353968v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference/reference_markers.hmm GCA_003539685.1_ASM353968v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:06:35,991] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:06:35,992] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg70c3bc45-d025-4e27-b9c2-290b51eb382c/GCA_003539685.1_ASM353968v1_genomic.fna.gz]
[2023-06-17 08:06:36,014] [INFO] Query marker FASTA was written to GCA_003539685.1_ASM353968v1_genomic.fna/markers.fasta
[2023-06-17 08:06:36,015] [INFO] Task started: Blastn
[2023-06-17 08:06:36,015] [INFO] Running command: blastn -query GCA_003539685.1_ASM353968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference/reference_markers.fasta -out GCA_003539685.1_ASM353968v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:06:36,607] [INFO] Task succeeded: Blastn
[2023-06-17 08:06:36,611] [INFO] Selected 22 target genomes.
[2023-06-17 08:06:36,611] [INFO] Target genome list was writen to GCA_003539685.1_ASM353968v1_genomic.fna/target_genomes.txt
[2023-06-17 08:06:36,614] [INFO] Task started: fastANI
[2023-06-17 08:06:36,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c3bc45-d025-4e27-b9c2-290b51eb382c/GCA_003539685.1_ASM353968v1_genomic.fna.gz --refList GCA_003539685.1_ASM353968v1_genomic.fna/target_genomes.txt --output GCA_003539685.1_ASM353968v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:06:44,365] [INFO] Task succeeded: fastANI
[2023-06-17 08:06:44,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:06:44,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:06:44,380] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-06-17 08:06:44,380] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 08:06:44,381] [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 acetotolerans	strain=JCM 3825	GCA_014648715.1	1600	1600	type	True	98.8466	298	341	95	conclusive
Lactobacillus acetotolerans	strain=DSM 20749	GCA_001436775.1	1600	1600	type	True	98.8198	294	341	95	conclusive
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	79.1747	125	341	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	79.1735	128	341	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	79.1571	131	341	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	79.1384	133	341	95	below_threshold
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	79.1202	132	341	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	79.0185	122	341	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.972	127	341	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	78.9479	133	341	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	78.9319	129	341	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	78.9016	130	341	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	78.8739	121	341	95	below_threshold
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	78.6541	123	341	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.5913	94	341	95	below_threshold
Lactobacillus kalixensis	strain=DSM 16043	GCA_001434335.1	227944	227944	type	True	78.5427	118	341	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 08:06:44,383] [INFO] DFAST Taxonomy check result was written to GCA_003539685.1_ASM353968v1_genomic.fna/tc_result.tsv
[2023-06-17 08:06:44,383] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:06:44,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:06:44,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference/checkm_data
[2023-06-17 08:06:44,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:06:44,401] [INFO] Task started: CheckM
[2023-06-17 08:06:44,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003539685.1_ASM353968v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003539685.1_ASM353968v1_genomic.fna/checkm_input GCA_003539685.1_ASM353968v1_genomic.fna/checkm_result
[2023-06-17 08:06:59,361] [INFO] Task succeeded: CheckM
[2023-06-17 08:06:59,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:06:59,389] [INFO] ===== Completeness check finished =====
[2023-06-17 08:06:59,390] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:06:59,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003539685.1_ASM353968v1_genomic.fna/markers.fasta)
[2023-06-17 08:06:59,391] [INFO] Task started: Blastn
[2023-06-17 08:06:59,391] [INFO] Running command: blastn -query GCA_003539685.1_ASM353968v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c5075bc-ff5a-468e-b97f-dc8b4f18c441/dqc_reference/reference_markers_gtdb.fasta -out GCA_003539685.1_ASM353968v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:07:00,195] [INFO] Task succeeded: Blastn
[2023-06-17 08:07:00,199] [INFO] Selected 18 target genomes.
[2023-06-17 08:07:00,199] [INFO] Target genome list was writen to GCA_003539685.1_ASM353968v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:07:00,203] [INFO] Task started: fastANI
[2023-06-17 08:07:00,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c3bc45-d025-4e27-b9c2-290b51eb382c/GCA_003539685.1_ASM353968v1_genomic.fna.gz --refList GCA_003539685.1_ASM353968v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003539685.1_ASM353968v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:07:06,834] [INFO] Task succeeded: fastANI
[2023-06-17 08:07:06,851] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:07:06,851] [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_001436775.1	s__Lactobacillus acetotolerans	98.8198	294	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.88	98.02	0.91	0.85	26	conclusive
GCF_000615445.1	s__Lactobacillus hamsteri	79.2077	123	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001436305.1	s__Lactobacillus ultunensis	79.1735	128	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	79.1202	132	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_002706375.1	s__Lactobacillus amylovorus	79.092	123	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001435325.1	s__Lactobacillus intestinalis	79.0663	127	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_000160855.1	s__Lactobacillus helveticus	78.9125	134	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_000615285.1	s__Lactobacillus kitasatonis	78.9016	130	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_018987235.1	s__Lactobacillus crispatus	78.8885	126	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCA_018883635.1	s__Lactobacillus pullistercoris	78.6957	112	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004009905.1	s__Lactobacillus xujianguonis	78.6887	122	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCA_910589675.1	s__Lactobacillus sp910589675	78.6394	90	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_001434335.1	s__Lactobacillus kalixensis	78.5427	118	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434975.1	s__Lactobacillus gallinarum	78.4867	132	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	78.4584	86	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
GCF_013346935.1	s__Lactobacillus melliventris	78.118	99	341	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
--------------------------------------------------------------------------------
[2023-06-17 08:07:06,853] [INFO] GTDB search result was written to GCA_003539685.1_ASM353968v1_genomic.fna/result_gtdb.tsv
[2023-06-17 08:07:06,854] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:07:06,858] [INFO] DFAST_QC result json was written to GCA_003539685.1_ASM353968v1_genomic.fna/dqc_result.json
[2023-06-17 08:07:06,859] [INFO] DFAST_QC completed!
[2023-06-17 08:07:06,859] [INFO] Total running time: 0h0m35s