[2024-01-24 14:32:34,365] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:34,369] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:34,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference
[2024-01-24 14:32:35,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:35,732] [INFO] Task started: Prodigal
[2024-01-24 14:32:35,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg6870e023-1ab9-4d41-8435-8f3989324ae5/GCF_003584685.1_ASM358468v1_genomic.fna.gz | prodigal -d GCF_003584685.1_ASM358468v1_genomic.fna/cds.fna -a GCF_003584685.1_ASM358468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:39,368] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:39,369] [INFO] Task started: HMMsearch
[2024-01-24 14:32:39,369] [INFO] Running command: hmmsearch --tblout GCF_003584685.1_ASM358468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference/reference_markers.hmm GCF_003584685.1_ASM358468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:39,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:39,641] [INFO] Found 6/6 markers.
[2024-01-24 14:32:39,684] [INFO] Query marker FASTA was written to GCF_003584685.1_ASM358468v1_genomic.fna/markers.fasta
[2024-01-24 14:32:39,685] [INFO] Task started: Blastn
[2024-01-24 14:32:39,685] [INFO] Running command: blastn -query GCF_003584685.1_ASM358468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference/reference_markers.fasta -out GCF_003584685.1_ASM358468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:40,339] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:40,343] [INFO] Selected 9 target genomes.
[2024-01-24 14:32:40,344] [INFO] Target genome list was writen to GCF_003584685.1_ASM358468v1_genomic.fna/target_genomes.txt
[2024-01-24 14:32:40,351] [INFO] Task started: fastANI
[2024-01-24 14:32:40,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg6870e023-1ab9-4d41-8435-8f3989324ae5/GCF_003584685.1_ASM358468v1_genomic.fna.gz --refList GCF_003584685.1_ASM358468v1_genomic.fna/target_genomes.txt --output GCF_003584685.1_ASM358468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:44,209] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:44,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:44,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:44,217] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:32:44,217] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:44,217] [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 paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	100.0	644	645	95	conclusive
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	99.9768	627	645	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	93.8119	542	645	95	below_threshold
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	93.7905	566	645	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	93.7464	570	645	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.4901	171	645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:44,219] [INFO] DFAST Taxonomy check result was written to GCF_003584685.1_ASM358468v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:44,219] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:44,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:44,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference/checkm_data
[2024-01-24 14:32:44,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:44,242] [INFO] Task started: CheckM
[2024-01-24 14:32:44,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003584685.1_ASM358468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003584685.1_ASM358468v1_genomic.fna/checkm_input GCF_003584685.1_ASM358468v1_genomic.fna/checkm_result
[2024-01-24 14:33:03,034] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:03,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:03,056] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:03,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:03,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003584685.1_ASM358468v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:03,057] [INFO] Task started: Blastn
[2024-01-24 14:33:03,057] [INFO] Running command: blastn -query GCF_003584685.1_ASM358468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg953af322-91d1-4c56-aaf2-17e44f9315fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_003584685.1_ASM358468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:03,829] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:03,833] [INFO] Selected 7 target genomes.
[2024-01-24 14:33:03,834] [INFO] Target genome list was writen to GCF_003584685.1_ASM358468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:03,840] [INFO] Task started: fastANI
[2024-01-24 14:33:03,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg6870e023-1ab9-4d41-8435-8f3989324ae5/GCF_003584685.1_ASM358468v1_genomic.fna.gz --refList GCF_003584685.1_ASM358468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003584685.1_ASM358468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:06,837] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:06,850] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:06,850] [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_003584685.1	s__Lactobacillus paragasseri	100.0	644	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	conclusive
GCF_000014425.1	s__Lactobacillus gasseri	93.7217	570	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_001436695.1	s__Lactobacillus taiwanensis	86.4062	472	645	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	85.5626	458	645	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	85.3616	465	645	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	84.3435	313	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_001435325.1	s__Lactobacillus intestinalis	79.0072	169	645	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:06,852] [INFO] GTDB search result was written to GCF_003584685.1_ASM358468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:06,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:06,855] [INFO] DFAST_QC result json was written to GCF_003584685.1_ASM358468v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:06,855] [INFO] DFAST_QC completed!
[2024-01-24 14:33:06,855] [INFO] Total running time: 0h0m32s