[2023-06-05 08:48:48,250] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:48:48,252] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:48:48,253] [INFO] DQC Reference Directory: /var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference
[2023-06-05 08:48:50,959] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:48:50,962] [INFO] Task started: Prodigal
[2023-06-05 08:48:50,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fd2447b-d8d1-488e-b2c6-4fd19ae70a25/GCA_934190895.1_ERR7738237_bin.49_genomic.fna.gz | prodigal -d GCA_934190895.1_ERR7738237_bin.49_genomic.fna/cds.fna -a GCA_934190895.1_ERR7738237_bin.49_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:48:54,398] [INFO] Task succeeded: Prodigal
[2023-06-05 08:48:54,398] [INFO] Task started: HMMsearch
[2023-06-05 08:48:54,398] [INFO] Running command: hmmsearch --tblout GCA_934190895.1_ERR7738237_bin.49_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference/reference_markers.hmm GCA_934190895.1_ERR7738237_bin.49_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:48:54,662] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:48:54,664] [INFO] Found 6/6 markers.
[2023-06-05 08:48:54,696] [INFO] Query marker FASTA was written to GCA_934190895.1_ERR7738237_bin.49_genomic.fna/markers.fasta
[2023-06-05 08:48:54,696] [INFO] Task started: Blastn
[2023-06-05 08:48:54,696] [INFO] Running command: blastn -query GCA_934190895.1_ERR7738237_bin.49_genomic.fna/markers.fasta -db /var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference/reference_markers.fasta -out GCA_934190895.1_ERR7738237_bin.49_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:48:55,342] [INFO] Task succeeded: Blastn
[2023-06-05 08:48:55,347] [INFO] Selected 10 target genomes.
[2023-06-05 08:48:55,347] [INFO] Target genome list was writen to GCA_934190895.1_ERR7738237_bin.49_genomic.fna/target_genomes.txt
[2023-06-05 08:48:55,378] [INFO] Task started: fastANI
[2023-06-05 08:48:55,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fd2447b-d8d1-488e-b2c6-4fd19ae70a25/GCA_934190895.1_ERR7738237_bin.49_genomic.fna.gz --refList GCA_934190895.1_ERR7738237_bin.49_genomic.fna/target_genomes.txt --output GCA_934190895.1_ERR7738237_bin.49_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:48:59,056] [INFO] Task succeeded: fastANI
[2023-06-05 08:48:59,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:48:59,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:48:59,068] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-05 08:48:59,069] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 08:48:59,069] [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_003307275.1	2107999	2107999	type	True	98.4737	560	614	95	conclusive
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	98.4309	565	614	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	93.6592	526	614	95	below_threshold
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	93.5547	539	614	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	93.5443	536	614	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.4055	180	614	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:48:59,071] [INFO] DFAST Taxonomy check result was written to GCA_934190895.1_ERR7738237_bin.49_genomic.fna/tc_result.tsv
[2023-06-05 08:48:59,071] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:48:59,072] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:48:59,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference/checkm_data
[2023-06-05 08:48:59,073] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:48:59,101] [INFO] Task started: CheckM
[2023-06-05 08:48:59,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934190895.1_ERR7738237_bin.49_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934190895.1_ERR7738237_bin.49_genomic.fna/checkm_input GCA_934190895.1_ERR7738237_bin.49_genomic.fna/checkm_result
[2023-06-05 08:49:18,263] [INFO] Task succeeded: CheckM
[2023-06-05 08:49:18,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:49:18,294] [INFO] ===== Completeness check finished =====
[2023-06-05 08:49:18,294] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:49:18,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934190895.1_ERR7738237_bin.49_genomic.fna/markers.fasta)
[2023-06-05 08:49:18,295] [INFO] Task started: Blastn
[2023-06-05 08:49:18,295] [INFO] Running command: blastn -query GCA_934190895.1_ERR7738237_bin.49_genomic.fna/markers.fasta -db /var/lib/cwl/stgf93a20cc-399e-4185-9dbe-443fdd7ff03d/dqc_reference/reference_markers_gtdb.fasta -out GCA_934190895.1_ERR7738237_bin.49_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:19,172] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:19,178] [INFO] Selected 7 target genomes.
[2023-06-05 08:49:19,178] [INFO] Target genome list was writen to GCA_934190895.1_ERR7738237_bin.49_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:49:19,187] [INFO] Task started: fastANI
[2023-06-05 08:49:19,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fd2447b-d8d1-488e-b2c6-4fd19ae70a25/GCA_934190895.1_ERR7738237_bin.49_genomic.fna.gz --refList GCA_934190895.1_ERR7738237_bin.49_genomic.fna/target_genomes_gtdb.txt --output GCA_934190895.1_ERR7738237_bin.49_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:49:22,336] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:22,350] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:49:22,350] [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	98.4693	564	614	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	93.5696	534	614	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	86.4534	465	614	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	85.51	448	614	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	85.3668	453	614	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	84.6202	304	614	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	79.1875	155	614	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
--------------------------------------------------------------------------------
[2023-06-05 08:49:22,352] [INFO] GTDB search result was written to GCA_934190895.1_ERR7738237_bin.49_genomic.fna/result_gtdb.tsv
[2023-06-05 08:49:22,353] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:49:22,356] [INFO] DFAST_QC result json was written to GCA_934190895.1_ERR7738237_bin.49_genomic.fna/dqc_result.json
[2023-06-05 08:49:22,356] [INFO] DFAST_QC completed!
[2023-06-05 08:49:22,356] [INFO] Total running time: 0h0m34s