[2023-06-08 00:35:18,904] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:35:18,906] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:35:18,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference
[2023-06-08 00:35:22,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:35:22,451] [INFO] Task started: Prodigal
[2023-06-08 00:35:22,451] [INFO] Running command: gunzip -c /var/lib/cwl/stgaeee9390-a999-4f78-aecc-154eda264490/GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:25,375] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:25,375] [INFO] Task started: HMMsearch
[2023-06-08 00:35:25,375] [INFO] Running command: hmmsearch --tblout GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference/reference_markers.hmm GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:25,624] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:25,625] [INFO] Found 6/6 markers.
[2023-06-08 00:35:25,662] [INFO] Query marker FASTA was written to GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:35:25,662] [INFO] Task started: Blastn
[2023-06-08 00:35:25,662] [INFO] Running command: blastn -query GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference/reference_markers.fasta -out GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:27,601] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:27,605] [INFO] Selected 13 target genomes.
[2023-06-08 00:35:27,606] [INFO] Target genome list was writen to GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:35:27,607] [INFO] Task started: fastANI
[2023-06-08 00:35:27,607] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeee9390-a999-4f78-aecc-154eda264490/GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:32,236] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:32,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:32,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:32,246] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:32,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:35:32,247] [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 johnsonii	strain=ATCC 33200	GCA_001433975.1	33959	33959	type	True	94.5169	422	530	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_000159355.1	33959	33959	type	True	94.4434	432	530	95	below_threshold
Lactobacillus taiwanensis	strain=DSM 21401	GCA_001436695.1	508451	508451	type	True	87.4071	406	530	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	85.168	384	530	95	below_threshold
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	85.1633	387	530	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	85.1397	384	530	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	85.1162	386	530	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	85.0612	395	530	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.3405	151	530	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:35:32,248] [INFO] DFAST Taxonomy check result was written to GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:35:32,249] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:32,249] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:32,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference/checkm_data
[2023-06-08 00:35:32,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:32,270] [INFO] Task started: CheckM
[2023-06-08 00:35:32,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:35:49,933] [INFO] Task succeeded: CheckM
[2023-06-08 00:35:49,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:35:49,955] [INFO] ===== Completeness check finished =====
[2023-06-08 00:35:49,955] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:35:49,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:35:49,956] [INFO] Task started: Blastn
[2023-06-08 00:35:49,956] [INFO] Running command: blastn -query GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dbb1e0e-cbfa-4fac-b4e4-7a4f375382e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:50,837] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:50,841] [INFO] Selected 7 target genomes.
[2023-06-08 00:35:50,841] [INFO] Target genome list was writen to GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:35:50,842] [INFO] Task started: fastANI
[2023-06-08 00:35:50,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeee9390-a999-4f78-aecc-154eda264490/GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:35:53,759] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:53,767] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 00:35:53,767] [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
GCA_910589175.1	s__Lactobacillus sp910589175	94.7735	435	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159355.1	s__Lactobacillus johnsonii	94.4434	432	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCA_910589675.1	s__Lactobacillus sp910589675	93.3284	292	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_001436695.1	s__Lactobacillus taiwanensis	87.4071	406	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_000014425.1	s__Lactobacillus gasseri	85.1397	384	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_003584685.1	s__Lactobacillus paragasseri	85.0612	395	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_017874575.1	s__Lactobacillus colini	79.3604	150	530	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 00:35:53,769] [INFO] GTDB search result was written to GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:35:53,770] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:35:53,774] [INFO] DFAST_QC result json was written to GCA_947369005.1_SRR16632758_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:35:53,775] [INFO] DFAST_QC completed!
[2023-06-08 00:35:53,775] [INFO] Total running time: 0h0m35s