[2024-01-24 11:58:56,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:56,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:56,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference
[2024-01-24 11:58:57,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,707] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg41f76bf5-f9d5-4bd2-ac0b-5501f6242c13/GCF_004009905.1_ASM400990v1_genomic.fna.gz | prodigal -d GCF_004009905.1_ASM400990v1_genomic.fna/cds.fna -a GCF_004009905.1_ASM400990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:01,951] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:01,951] [INFO] Task started: HMMsearch
[2024-01-24 11:59:01,952] [INFO] Running command: hmmsearch --tblout GCF_004009905.1_ASM400990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference/reference_markers.hmm GCF_004009905.1_ASM400990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:02,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:02,288] [INFO] Found 6/6 markers.
[2024-01-24 11:59:02,326] [INFO] Query marker FASTA was written to GCF_004009905.1_ASM400990v1_genomic.fna/markers.fasta
[2024-01-24 11:59:02,326] [INFO] Task started: Blastn
[2024-01-24 11:59:02,326] [INFO] Running command: blastn -query GCF_004009905.1_ASM400990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference/reference_markers.fasta -out GCF_004009905.1_ASM400990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:02,955] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:02,958] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:02,959] [INFO] Target genome list was writen to GCF_004009905.1_ASM400990v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:03,032] [INFO] Task started: fastANI
[2024-01-24 11:59:03,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f76bf5-f9d5-4bd2-ac0b-5501f6242c13/GCF_004009905.1_ASM400990v1_genomic.fna.gz --refList GCF_004009905.1_ASM400990v1_genomic.fna/target_genomes.txt --output GCF_004009905.1_ASM400990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:09,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:09,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:09,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:09,879] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:09,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:09,879] [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 xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	100.0	697	699	95	conclusive
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	81.0664	268	699	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	81.0386	270	699	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	80.8704	257	699	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_000178475.1	83683	83683	type	True	80.7769	222	699	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	80.7326	234	699	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	80.7175	237	699	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	80.6914	232	699	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	80.6415	228	699	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	80.6391	253	699	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	80.6041	228	699	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	80.5535	268	699	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	80.5453	274	699	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_001433985.1	1604	1604	type	True	80.3869	255	699	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	80.1396	257	699	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	80.1258	247	699	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.1113	247	699	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.6978	120	699	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.5287	105	699	95	below_threshold
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	78.4716	122	699	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:09,884] [INFO] DFAST Taxonomy check result was written to GCF_004009905.1_ASM400990v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:09,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:09,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:09,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference/checkm_data
[2024-01-24 11:59:09,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:09,915] [INFO] Task started: CheckM
[2024-01-24 11:59:09,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004009905.1_ASM400990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004009905.1_ASM400990v1_genomic.fna/checkm_input GCF_004009905.1_ASM400990v1_genomic.fna/checkm_result
[2024-01-24 11:59:30,573] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:30,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:30,608] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:30,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:30,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004009905.1_ASM400990v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:30,609] [INFO] Task started: Blastn
[2024-01-24 11:59:30,609] [INFO] Running command: blastn -query GCF_004009905.1_ASM400990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd5bdaa4-fe58-4369-b4f0-a5c9d59f6b5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004009905.1_ASM400990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:31,433] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:31,437] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:31,437] [INFO] Target genome list was writen to GCF_004009905.1_ASM400990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:31,449] [INFO] Task started: fastANI
[2024-01-24 11:59:31,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f76bf5-f9d5-4bd2-ac0b-5501f6242c13/GCF_004009905.1_ASM400990v1_genomic.fna.gz --refList GCF_004009905.1_ASM400990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004009905.1_ASM400990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:37,294] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:37,306] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:37,307] [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_004009905.1	s__Lactobacillus xujianguonis	100.0	697	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	conclusive
GCF_000615445.1	s__Lactobacillus hamsteri	81.0519	269	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001434975.1	s__Lactobacillus gallinarum	80.8814	254	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000178475.1	s__Lactobacillus amylolyticus	80.7769	222	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_000615285.1	s__Lactobacillus kitasatonis	80.7202	234	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_002706375.1	s__Lactobacillus amylovorus	80.5535	268	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000160855.1	s__Lactobacillus helveticus	80.5313	274	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001434335.1	s__Lactobacillus kalixensis	80.3579	257	699	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	80.2952	264	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_001591845.1	s__Lactobacillus acidophilus	80.2002	228	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_001435325.1	s__Lactobacillus intestinalis	80.1537	243	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_007570935.1	s__Lactobacillus sp007570935	80.1423	199	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436305.1	s__Lactobacillus ultunensis	80.1258	247	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_007095465.1	s__Lactobacillus mulieris	78.4616	123	699	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:37,308] [INFO] GTDB search result was written to GCF_004009905.1_ASM400990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:37,309] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:37,313] [INFO] DFAST_QC result json was written to GCF_004009905.1_ASM400990v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:37,313] [INFO] DFAST_QC completed!
[2024-01-24 11:59:37,313] [INFO] Total running time: 0h0m41s