[2024-01-24 13:25:47,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference
[2024-01-24 13:25:49,078] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,079] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,079] [INFO] Running command: gunzip -c /var/lib/cwl/stgc20a3337-ca82-4e21-a582-1c979dc6e6d6/GCF_001435975.1_ASM143597v1_genomic.fna.gz | prodigal -d GCF_001435975.1_ASM143597v1_genomic.fna/cds.fna -a GCF_001435975.1_ASM143597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:58,273] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:58,273] [INFO] Task started: HMMsearch
[2024-01-24 13:25:58,273] [INFO] Running command: hmmsearch --tblout GCF_001435975.1_ASM143597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference/reference_markers.hmm GCF_001435975.1_ASM143597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:58,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:58,539] [INFO] Found 6/6 markers.
[2024-01-24 13:25:58,567] [INFO] Query marker FASTA was written to GCF_001435975.1_ASM143597v1_genomic.fna/markers.fasta
[2024-01-24 13:25:58,568] [INFO] Task started: Blastn
[2024-01-24 13:25:58,568] [INFO] Running command: blastn -query GCF_001435975.1_ASM143597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference/reference_markers.fasta -out GCF_001435975.1_ASM143597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:59,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:59,176] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:59,176] [INFO] Target genome list was writen to GCF_001435975.1_ASM143597v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:59,183] [INFO] Task started: fastANI
[2024-01-24 13:25:59,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgc20a3337-ca82-4e21-a582-1c979dc6e6d6/GCF_001435975.1_ASM143597v1_genomic.fna.gz --refList GCF_001435975.1_ASM143597v1_genomic.fna/target_genomes.txt --output GCF_001435975.1_ASM143597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:06,546] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:06,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:06,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:06,557] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:06,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:06,558] [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
Secundilactobacillus collinoides	strain=DSM 20515	GCA_001435975.1	33960	33960	type	True	100.0	1154	1155	95	conclusive
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	99.8272	1095	1155	95	conclusive
Secundilactobacillus paracollinoides	strain=DSM 15502	GCA_001435115.1	240427	240427	type	True	82.5688	710	1155	95	below_threshold
Secundilactobacillus paracollinoides	strain=JCM 11969	GCA_001311135.1	240427	240427	type	True	82.511	708	1155	95	below_threshold
Secundilactobacillus mixtipabuli	strain=IWT30	GCA_002217925.1	1435342	1435342	type	True	79.557	181	1155	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	79.4143	160	1155	95	below_threshold
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	79.2864	206	1155	95	below_threshold
Secundilactobacillus oryzae	strain=JCM 18671	GCA_001311525.1	1202668	1202668	type	True	79.2057	81	1155	95	below_threshold
Secundilactobacillus similis	strain=JCM 2765	GCA_001311075.1	414682	414682	type	True	79.0157	235	1155	95	below_threshold
Secundilactobacillus similis	strain=DSM 23365	GCA_001436595.1	414682	414682	type	True	78.9039	241	1155	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	78.7058	189	1155	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	78.6832	178	1155	95	below_threshold
Secundilactobacillus yichangensis	strain=F79-211-2	GCA_016861565.1	2799580	2799580	type	True	78.5366	190	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:06,559] [INFO] DFAST Taxonomy check result was written to GCF_001435975.1_ASM143597v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:06,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:06,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:06,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference/checkm_data
[2024-01-24 13:26:06,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:06,602] [INFO] Task started: CheckM
[2024-01-24 13:26:06,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435975.1_ASM143597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435975.1_ASM143597v1_genomic.fna/checkm_input GCF_001435975.1_ASM143597v1_genomic.fna/checkm_result
[2024-01-24 13:26:38,936] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:38,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:38,952] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:38,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:38,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435975.1_ASM143597v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:38,954] [INFO] Task started: Blastn
[2024-01-24 13:26:38,954] [INFO] Running command: blastn -query GCF_001435975.1_ASM143597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2abaf26b-0d92-4c62-878d-ea0663d48572/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435975.1_ASM143597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:39,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:39,700] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:39,700] [INFO] Target genome list was writen to GCF_001435975.1_ASM143597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:39,708] [INFO] Task started: fastANI
[2024-01-24 13:26:39,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgc20a3337-ca82-4e21-a582-1c979dc6e6d6/GCF_001435975.1_ASM143597v1_genomic.fna.gz --refList GCF_001435975.1_ASM143597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435975.1_ASM143597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:46,660] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:46,675] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:46,675] [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_001435975.1	s__Secundilactobacillus collinoides	100.0	1154	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.82	99.79	0.97	0.94	3	conclusive
GCF_001311135.1	s__Secundilactobacillus paracollinoides	82.5472	703	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.57	99.45	0.95	0.89	5	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	79.557	181	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002583405.1	s__Secundilactobacillus silagincola	79.4618	178	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_012641075.1	s__Secundilactobacillus sp012641075	79.4143	160	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405185.1	s__Secundilactobacillus sp005405185	79.2987	205	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217985.1	s__Secundilactobacillus pentosiphilus	79.0561	186	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.11	97.11	0.89	0.89	2	-
GCF_001311075.1	s__Secundilactobacillus similis	79.0072	236	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.93	99.93	0.98	0.98	2	-
GCF_002217945.1	s__Secundilactobacillus silagei	78.5486	194	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	-
GCF_016861565.1	s__Secundilactobacillus sp016861565	78.5366	190	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436395.1	s__Secundilactobacillus malefermentans	78.1965	70	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.75	99.27	0.97	0.94	4	-
GCF_009720675.1	s__Secundilactobacillus folii	78.1364	168	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435525.1	s__Levilactobacillus koreensis	78.0837	102	1155	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:46,677] [INFO] GTDB search result was written to GCF_001435975.1_ASM143597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:46,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:46,680] [INFO] DFAST_QC result json was written to GCF_001435975.1_ASM143597v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:46,680] [INFO] DFAST_QC completed!
[2024-01-24 13:26:46,681] [INFO] Total running time: 0h0m59s