[2023-06-05 19:01:48,550] [INFO] DFAST_QC pipeline started.
[2023-06-05 19:01:48,553] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 19:01:48,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference
[2023-06-05 19:01:50,394] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 19:01:50,395] [INFO] Task started: Prodigal
[2023-06-05 19:01:50,395] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a073bf4-63d5-40ee-b5d2-f75e2d9b3c60/GCA_004551705.1_ASM455170v1_genomic.fna.gz | prodigal -d GCA_004551705.1_ASM455170v1_genomic.fna/cds.fna -a GCA_004551705.1_ASM455170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 19:01:53,464] [INFO] Task succeeded: Prodigal
[2023-06-05 19:01:53,465] [INFO] Task started: HMMsearch
[2023-06-05 19:01:53,466] [INFO] Running command: hmmsearch --tblout GCA_004551705.1_ASM455170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference/reference_markers.hmm GCA_004551705.1_ASM455170v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 19:01:53,709] [INFO] Task succeeded: HMMsearch
[2023-06-05 19:01:53,711] [INFO] Found 6/6 markers.
[2023-06-05 19:01:53,745] [INFO] Query marker FASTA was written to GCA_004551705.1_ASM455170v1_genomic.fna/markers.fasta
[2023-06-05 19:01:53,746] [INFO] Task started: Blastn
[2023-06-05 19:01:53,746] [INFO] Running command: blastn -query GCA_004551705.1_ASM455170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference/reference_markers.fasta -out GCA_004551705.1_ASM455170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:01:54,675] [INFO] Task succeeded: Blastn
[2023-06-05 19:01:54,680] [INFO] Selected 26 target genomes.
[2023-06-05 19:01:54,680] [INFO] Target genome list was writen to GCA_004551705.1_ASM455170v1_genomic.fna/target_genomes.txt
[2023-06-05 19:01:54,696] [INFO] Task started: fastANI
[2023-06-05 19:01:54,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a073bf4-63d5-40ee-b5d2-f75e2d9b3c60/GCA_004551705.1_ASM455170v1_genomic.fna.gz --refList GCA_004551705.1_ASM455170v1_genomic.fna/target_genomes.txt --output GCA_004551705.1_ASM455170v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 19:02:08,507] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:08,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 19:02:08,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 19:02:08,521] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 19:02:08,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 19:02:08,521] [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 coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	79.34	87	297	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	78.6347	85	297	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.6326	80	297	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.274	85	297	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.2681	60	297	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.7899	63	297	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.7319	66	297	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.7266	61	297	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.7155	60	297	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 19:02:08,523] [INFO] DFAST Taxonomy check result was written to GCA_004551705.1_ASM455170v1_genomic.fna/tc_result.tsv
[2023-06-05 19:02:08,524] [INFO] ===== Taxonomy check completed =====
[2023-06-05 19:02:08,524] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 19:02:08,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference/checkm_data
[2023-06-05 19:02:08,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 19:02:08,562] [INFO] Task started: CheckM
[2023-06-05 19:02:08,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004551705.1_ASM455170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004551705.1_ASM455170v1_genomic.fna/checkm_input GCA_004551705.1_ASM455170v1_genomic.fna/checkm_result
[2023-06-05 19:02:25,073] [INFO] Task succeeded: CheckM
[2023-06-05 19:02:25,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 19:02:25,096] [INFO] ===== Completeness check finished =====
[2023-06-05 19:02:25,097] [INFO] ===== Start GTDB Search =====
[2023-06-05 19:02:25,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004551705.1_ASM455170v1_genomic.fna/markers.fasta)
[2023-06-05 19:02:25,097] [INFO] Task started: Blastn
[2023-06-05 19:02:25,098] [INFO] Running command: blastn -query GCA_004551705.1_ASM455170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80356fab-9790-45eb-bfba-96a20dfc6f20/dqc_reference/reference_markers_gtdb.fasta -out GCA_004551705.1_ASM455170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 19:02:26,275] [INFO] Task succeeded: Blastn
[2023-06-05 19:02:26,278] [INFO] Selected 13 target genomes.
[2023-06-05 19:02:26,278] [INFO] Target genome list was writen to GCA_004551705.1_ASM455170v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 19:02:26,292] [INFO] Task started: fastANI
[2023-06-05 19:02:26,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a073bf4-63d5-40ee-b5d2-f75e2d9b3c60/GCA_004551705.1_ASM455170v1_genomic.fna.gz --refList GCA_004551705.1_ASM455170v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004551705.1_ASM455170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 19:02:30,401] [INFO] Task succeeded: fastANI
[2023-06-05 19:02:30,415] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 19:02:30,415] [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_018918025.1	s__ER4 sp900317525	97.7385	284	297	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.58	97.23	0.91	0.84	22	conclusive
GCA_002437735.1	s__ER4 sp002437735	94.6986	226	297	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.63	99.63	0.85	0.85	2	-
GCA_900552375.1	s__ER4 sp900552375	88.3655	249	297	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900546295.1	s__ER4 sp900546295	82.334	188	297	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_002405995.1	s__ER4 sp002405995	82.2624	201	297	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_900552015.1	s__ER4 sp900552015	82.064	184	297	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	81.9982	193	297	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_900763705.1	s__ER4 sp900763705	81.7261	170	297	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_900556145.1	s__ER4 sp900556145	81.6882	138	297	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_900768135.1	s__ER4 sp900768135	81.4549	188	297	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_016295615.1	s__ER4 sp016295615	80.4257	147	297	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.52	97.90	0.85	0.84	3	-
GCA_015068395.1	s__ER4 sp015068395	79.0984	138	297	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 19:02:30,417] [INFO] GTDB search result was written to GCA_004551705.1_ASM455170v1_genomic.fna/result_gtdb.tsv
[2023-06-05 19:02:30,418] [INFO] ===== GTDB Search completed =====
[2023-06-05 19:02:30,422] [INFO] DFAST_QC result json was written to GCA_004551705.1_ASM455170v1_genomic.fna/dqc_result.json
[2023-06-05 19:02:30,422] [INFO] DFAST_QC completed!
[2023-06-05 19:02:30,423] [INFO] Total running time: 0h0m42s