[2023-06-28 18:17:10,875] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:17:10,878] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:17:10,878] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference
[2023-06-28 18:17:12,153] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:17:12,154] [INFO] Task started: Prodigal
[2023-06-28 18:17:12,155] [INFO] Running command: gunzip -c /var/lib/cwl/stg333b0f05-c91d-4ac1-bad3-9659b48721e8/GCA_944385455.1_E07_bin169_genomic.fna.gz | prodigal -d GCA_944385455.1_E07_bin169_genomic.fna/cds.fna -a GCA_944385455.1_E07_bin169_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:17:16,813] [INFO] Task succeeded: Prodigal
[2023-06-28 18:17:16,813] [INFO] Task started: HMMsearch
[2023-06-28 18:17:16,814] [INFO] Running command: hmmsearch --tblout GCA_944385455.1_E07_bin169_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference/reference_markers.hmm GCA_944385455.1_E07_bin169_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:17:17,054] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:17:17,055] [INFO] Found 6/6 markers.
[2023-06-28 18:17:17,076] [INFO] Query marker FASTA was written to GCA_944385455.1_E07_bin169_genomic.fna/markers.fasta
[2023-06-28 18:17:17,076] [INFO] Task started: Blastn
[2023-06-28 18:17:17,076] [INFO] Running command: blastn -query GCA_944385455.1_E07_bin169_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference/reference_markers.fasta -out GCA_944385455.1_E07_bin169_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:17:17,840] [INFO] Task succeeded: Blastn
[2023-06-28 18:17:17,844] [INFO] Selected 11 target genomes.
[2023-06-28 18:17:17,845] [INFO] Target genome list was writen to GCA_944385455.1_E07_bin169_genomic.fna/target_genomes.txt
[2023-06-28 18:17:17,846] [INFO] Task started: fastANI
[2023-06-28 18:17:17,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg333b0f05-c91d-4ac1-bad3-9659b48721e8/GCA_944385455.1_E07_bin169_genomic.fna.gz --refList GCA_944385455.1_E07_bin169_genomic.fna/target_genomes.txt --output GCA_944385455.1_E07_bin169_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:17:23,955] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:23,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:17:23,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:17:23,971] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:17:23,971] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:17:23,971] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	80.7832	299	474	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.0175	191	474	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.7522	190	474	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.0443	124	474	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.0319	138	474	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.0096	136	474	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.6718	104	474	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.1366	90	474	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:17:23,976] [INFO] DFAST Taxonomy check result was written to GCA_944385455.1_E07_bin169_genomic.fna/tc_result.tsv
[2023-06-28 18:17:23,977] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:17:23,977] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:17:23,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference/checkm_data
[2023-06-28 18:17:23,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:17:24,002] [INFO] Task started: CheckM
[2023-06-28 18:17:24,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385455.1_E07_bin169_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385455.1_E07_bin169_genomic.fna/checkm_input GCA_944385455.1_E07_bin169_genomic.fna/checkm_result
[2023-06-28 18:17:45,129] [INFO] Task succeeded: CheckM
[2023-06-28 18:17:45,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:17:45,163] [INFO] ===== Completeness check finished =====
[2023-06-28 18:17:45,163] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:17:45,163] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385455.1_E07_bin169_genomic.fna/markers.fasta)
[2023-06-28 18:17:45,164] [INFO] Task started: Blastn
[2023-06-28 18:17:45,164] [INFO] Running command: blastn -query GCA_944385455.1_E07_bin169_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bcd15d7-60f4-44e9-8ce2-b3232a2bc011/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385455.1_E07_bin169_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:17:46,317] [INFO] Task succeeded: Blastn
[2023-06-28 18:17:46,326] [INFO] Selected 17 target genomes.
[2023-06-28 18:17:46,327] [INFO] Target genome list was writen to GCA_944385455.1_E07_bin169_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:17:46,355] [INFO] Task started: fastANI
[2023-06-28 18:17:46,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg333b0f05-c91d-4ac1-bad3-9659b48721e8/GCA_944385455.1_E07_bin169_genomic.fna.gz --refList GCA_944385455.1_E07_bin169_genomic.fna/target_genomes_gtdb.txt --output GCA_944385455.1_E07_bin169_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:17:54,835] [INFO] Task succeeded: fastANI
[2023-06-28 18:17:54,854] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:17:54,854] [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_900544955.1	s__Dysosmobacter sp900544955	83.4766	313	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228705.1	s__Dysosmobacter sp018228705	82.6168	312	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	82.2827	297	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	81.936	291	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	81.9098	278	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	81.898	290	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_900548505.1	s__Dysosmobacter sp900548505	81.8884	253	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118505.1	s__Dysosmobacter excrementavium	81.8553	272	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558115.1	s__Dysosmobacter sp004558115	81.7831	223	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546705.1	s__Dysosmobacter sp900546705	81.7692	239	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403435.2	s__Dysosmobacter sp000403435	80.8735	266	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.32	98.32	0.80	0.80	2	-
GCF_005121165.2	s__Dysosmobacter welbionis	80.7621	300	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCA_016293265.1	s__Dysosmobacter sp016293265	80.7027	195	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576865.1	s__Dysosmobacter sp910576865	80.4054	232	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586735.1	s__Dysosmobacter sp910586735	79.8462	237	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583695.1	s__Dysosmobacter sp910583695	79.507	229	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579365.1	s__Dysosmobacter sp910579365	79.4597	235	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:17:54,856] [INFO] GTDB search result was written to GCA_944385455.1_E07_bin169_genomic.fna/result_gtdb.tsv
[2023-06-28 18:17:54,857] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:17:54,861] [INFO] DFAST_QC result json was written to GCA_944385455.1_E07_bin169_genomic.fna/dqc_result.json
[2023-06-28 18:17:54,861] [INFO] DFAST_QC completed!
[2023-06-28 18:17:54,861] [INFO] Total running time: 0h0m44s