[2023-06-13 13:00:28,136] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:28,144] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:28,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference
[2023-06-13 13:00:29,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:29,498] [INFO] Task started: Prodigal
[2023-06-13 13:00:29,499] [INFO] Running command: gunzip -c /var/lib/cwl/stgc60d5ca6-28f4-4a88-882f-42ea69ecb40b/GCA_022782825.1_ASM2278282v1_genomic.fna.gz | prodigal -d GCA_022782825.1_ASM2278282v1_genomic.fna/cds.fna -a GCA_022782825.1_ASM2278282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:34,027] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:34,028] [INFO] Task started: HMMsearch
[2023-06-13 13:00:34,028] [INFO] Running command: hmmsearch --tblout GCA_022782825.1_ASM2278282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference/reference_markers.hmm GCA_022782825.1_ASM2278282v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:34,265] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:34,267] [INFO] Found 6/6 markers.
[2023-06-13 13:00:34,336] [INFO] Query marker FASTA was written to GCA_022782825.1_ASM2278282v1_genomic.fna/markers.fasta
[2023-06-13 13:00:34,336] [INFO] Task started: Blastn
[2023-06-13 13:00:34,336] [INFO] Running command: blastn -query GCA_022782825.1_ASM2278282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference/reference_markers.fasta -out GCA_022782825.1_ASM2278282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:35,035] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:35,040] [INFO] Selected 27 target genomes.
[2023-06-13 13:00:35,040] [INFO] Target genome list was writen to GCA_022782825.1_ASM2278282v1_genomic.fna/target_genomes.txt
[2023-06-13 13:00:35,044] [INFO] Task started: fastANI
[2023-06-13 13:00:35,044] [INFO] Running command: fastANI --query /var/lib/cwl/stgc60d5ca6-28f4-4a88-882f-42ea69ecb40b/GCA_022782825.1_ASM2278282v1_genomic.fna.gz --refList GCA_022782825.1_ASM2278282v1_genomic.fna/target_genomes.txt --output GCA_022782825.1_ASM2278282v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:00:48,781] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:48,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:00:48,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:00:48,791] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:00:48,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:00:48,792] [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
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.0918	100	474	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.9411	106	474	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.7214	91	474	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.6657	89	474	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.5325	53	474	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.4853	65	474	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.1928	73	474	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.9899	73	474	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.9106	72	474	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:00:48,794] [INFO] DFAST Taxonomy check result was written to GCA_022782825.1_ASM2278282v1_genomic.fna/tc_result.tsv
[2023-06-13 13:00:48,795] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:00:48,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:00:48,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference/checkm_data
[2023-06-13 13:00:48,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:00:48,820] [INFO] Task started: CheckM
[2023-06-13 13:00:48,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022782825.1_ASM2278282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022782825.1_ASM2278282v1_genomic.fna/checkm_input GCA_022782825.1_ASM2278282v1_genomic.fna/checkm_result
[2023-06-13 13:01:09,100] [INFO] Task succeeded: CheckM
[2023-06-13 13:01:09,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:01:09,123] [INFO] ===== Completeness check finished =====
[2023-06-13 13:01:09,124] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:01:09,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022782825.1_ASM2278282v1_genomic.fna/markers.fasta)
[2023-06-13 13:01:09,124] [INFO] Task started: Blastn
[2023-06-13 13:01:09,124] [INFO] Running command: blastn -query GCA_022782825.1_ASM2278282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57614b14-1eb7-4d21-a169-f688f47bc43c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022782825.1_ASM2278282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:01:10,143] [INFO] Task succeeded: Blastn
[2023-06-13 13:01:10,148] [INFO] Selected 9 target genomes.
[2023-06-13 13:01:10,148] [INFO] Target genome list was writen to GCA_022782825.1_ASM2278282v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:01:10,181] [INFO] Task started: fastANI
[2023-06-13 13:01:10,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgc60d5ca6-28f4-4a88-882f-42ea69ecb40b/GCA_022782825.1_ASM2278282v1_genomic.fna.gz --refList GCA_022782825.1_ASM2278282v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022782825.1_ASM2278282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:01:13,829] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:13,843] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:01:13,844] [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_000765235.1	s__ER4 sp000765235	97.2411	441	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.82	96.40	0.83	0.70	19	conclusive
GCA_900552015.1	s__ER4 sp900552015	90.5597	369	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900550165.1	s__ER4 sp900550165	89.0059	346	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.79	96.53	0.85	0.84	4	-
GCA_003522105.1	s__ER4 sp003522105	88.2167	337	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.35	97.09	0.78	0.74	7	-
GCA_900763705.1	s__ER4 sp900763705	88.1553	299	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546295.1	s__ER4 sp900546295	87.505	347	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.01	98.01	0.87	0.87	2	-
GCA_900556145.1	s__ER4 sp900556145	86.5044	232	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405995.1	s__ER4 sp002405995	85.4621	313	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_900549405.1	s__Lawsonibacter sp900549405	77.5682	67	474	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-13 13:01:13,846] [INFO] GTDB search result was written to GCA_022782825.1_ASM2278282v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:01:13,847] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:01:13,850] [INFO] DFAST_QC result json was written to GCA_022782825.1_ASM2278282v1_genomic.fna/dqc_result.json
[2023-06-13 13:01:13,851] [INFO] DFAST_QC completed!
[2023-06-13 13:01:13,851] [INFO] Total running time: 0h0m46s