[2024-01-24 13:25:42,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:42,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:42,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference
[2024-01-24 13:25:43,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:43,671] [INFO] Task started: Prodigal
[2024-01-24 13:25:43,671] [INFO] Running command: gunzip -c /var/lib/cwl/stgd10dcae8-d596-4cb7-b679-2e980d83383c/GCF_008868295.1_ASM886829v1_genomic.fna.gz | prodigal -d GCF_008868295.1_ASM886829v1_genomic.fna/cds.fna -a GCF_008868295.1_ASM886829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:46,909] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:46,910] [INFO] Task started: HMMsearch
[2024-01-24 13:25:46,910] [INFO] Running command: hmmsearch --tblout GCF_008868295.1_ASM886829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference/reference_markers.hmm GCF_008868295.1_ASM886829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:47,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:47,178] [INFO] Found 6/6 markers.
[2024-01-24 13:25:47,211] [INFO] Query marker FASTA was written to GCF_008868295.1_ASM886829v1_genomic.fna/markers.fasta
[2024-01-24 13:25:47,212] [INFO] Task started: Blastn
[2024-01-24 13:25:47,212] [INFO] Running command: blastn -query GCF_008868295.1_ASM886829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference/reference_markers.fasta -out GCF_008868295.1_ASM886829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:47,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:47,846] [INFO] Selected 10 target genomes.
[2024-01-24 13:25:47,847] [INFO] Target genome list was writen to GCF_008868295.1_ASM886829v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:47,884] [INFO] Task started: fastANI
[2024-01-24 13:25:47,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10dcae8-d596-4cb7-b679-2e980d83383c/GCF_008868295.1_ASM886829v1_genomic.fna.gz --refList GCF_008868295.1_ASM886829v1_genomic.fna/target_genomes.txt --output GCF_008868295.1_ASM886829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:51,948] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:51,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:51,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:51,956] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:25:51,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:51,956] [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 gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	100.0	592	594	95	conclusive
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	99.999	593	594	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	99.9989	593	594	95	conclusive
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	93.8137	545	594	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	93.7645	553	594	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.1976	169	594	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.8349	167	594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:51,958] [INFO] DFAST Taxonomy check result was written to GCF_008868295.1_ASM886829v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:51,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:51,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:51,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference/checkm_data
[2024-01-24 13:25:51,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:51,984] [INFO] Task started: CheckM
[2024-01-24 13:25:51,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008868295.1_ASM886829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008868295.1_ASM886829v1_genomic.fna/checkm_input GCF_008868295.1_ASM886829v1_genomic.fna/checkm_result
[2024-01-24 13:26:09,840] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:09,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:09,855] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:09,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:09,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008868295.1_ASM886829v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:09,856] [INFO] Task started: Blastn
[2024-01-24 13:26:09,856] [INFO] Running command: blastn -query GCF_008868295.1_ASM886829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbee25785-d083-423b-9593-ee8e907eb82d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008868295.1_ASM886829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:10,634] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:10,639] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:10,639] [INFO] Target genome list was writen to GCF_008868295.1_ASM886829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:10,646] [INFO] Task started: fastANI
[2024-01-24 13:26:10,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10dcae8-d596-4cb7-b679-2e980d83383c/GCF_008868295.1_ASM886829v1_genomic.fna.gz --refList GCF_008868295.1_ASM886829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008868295.1_ASM886829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:13,709] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:13,721] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:13,722] [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_000014425.1	s__Lactobacillus gasseri	99.9989	593	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	conclusive
GCF_003584685.1	s__Lactobacillus paragasseri	93.7645	553	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_001436695.1	s__Lactobacillus taiwanensis	86.0592	449	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_000159355.1	s__Lactobacillus johnsonii	85.5828	454	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCA_910589175.1	s__Lactobacillus sp910589175	85.4508	446	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589675.1	s__Lactobacillus sp910589675	84.6959	295	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCA_014803905.1	s__Lactobacillus sp014803905	79.4306	114	594	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	79.0068	145	594	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:13,728] [INFO] GTDB search result was written to GCF_008868295.1_ASM886829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:13,729] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:13,734] [INFO] DFAST_QC result json was written to GCF_008868295.1_ASM886829v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:13,734] [INFO] DFAST_QC completed!
[2024-01-24 13:26:13,734] [INFO] Total running time: 0h0m31s