[2023-06-05 03:38:36,628] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:38:36,630] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:38:36,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference
[2023-06-05 03:38:37,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:38:37,815] [INFO] Task started: Prodigal
[2023-06-05 03:38:37,815] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa190759-0a29-4a42-865a-772fed58849e/GCA_004552005.1_ASM455200v1_genomic.fna.gz | prodigal -d GCA_004552005.1_ASM455200v1_genomic.fna/cds.fna -a GCA_004552005.1_ASM455200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:38:42,820] [INFO] Task succeeded: Prodigal
[2023-06-05 03:38:42,821] [INFO] Task started: HMMsearch
[2023-06-05 03:38:42,821] [INFO] Running command: hmmsearch --tblout GCA_004552005.1_ASM455200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference/reference_markers.hmm GCA_004552005.1_ASM455200v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:38:43,046] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:38:43,048] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaa190759-0a29-4a42-865a-772fed58849e/GCA_004552005.1_ASM455200v1_genomic.fna.gz]
[2023-06-05 03:38:43,072] [INFO] Query marker FASTA was written to GCA_004552005.1_ASM455200v1_genomic.fna/markers.fasta
[2023-06-05 03:38:43,072] [INFO] Task started: Blastn
[2023-06-05 03:38:43,072] [INFO] Running command: blastn -query GCA_004552005.1_ASM455200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference/reference_markers.fasta -out GCA_004552005.1_ASM455200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:38:43,751] [INFO] Task succeeded: Blastn
[2023-06-05 03:38:43,755] [INFO] Selected 25 target genomes.
[2023-06-05 03:38:43,755] [INFO] Target genome list was writen to GCA_004552005.1_ASM455200v1_genomic.fna/target_genomes.txt
[2023-06-05 03:38:43,756] [INFO] Task started: fastANI
[2023-06-05 03:38:43,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa190759-0a29-4a42-865a-772fed58849e/GCA_004552005.1_ASM455200v1_genomic.fna.gz --refList GCA_004552005.1_ASM455200v1_genomic.fna/target_genomes.txt --output GCA_004552005.1_ASM455200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:38:59,515] [INFO] Task succeeded: fastANI
[2023-06-05 03:38:59,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:38:59,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:38:59,532] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:38:59,532] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:38:59,533] [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	77.1878	71	595	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.0969	67	595	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.0494	71	595	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.0097	67	595	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.8738	67	595	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.8632	71	595	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.5849	73	595	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.4345	58	595	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.3302	71	595	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.0842	54	595	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	75.9364	54	595	95	below_threshold
Sporobacter termitidis	strain=DSM 10068	GCA_900130065.1	44749	44749	type	True	75.8896	61	595	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	74.8345	53	595	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:38:59,535] [INFO] DFAST Taxonomy check result was written to GCA_004552005.1_ASM455200v1_genomic.fna/tc_result.tsv
[2023-06-05 03:38:59,536] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:38:59,536] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:38:59,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference/checkm_data
[2023-06-05 03:38:59,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:38:59,560] [INFO] Task started: CheckM
[2023-06-05 03:38:59,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004552005.1_ASM455200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004552005.1_ASM455200v1_genomic.fna/checkm_input GCA_004552005.1_ASM455200v1_genomic.fna/checkm_result
[2023-06-05 03:39:20,943] [INFO] Task succeeded: CheckM
[2023-06-05 03:39:20,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 6.82%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:39:20,969] [INFO] ===== Completeness check finished =====
[2023-06-05 03:39:20,969] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:39:20,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004552005.1_ASM455200v1_genomic.fna/markers.fasta)
[2023-06-05 03:39:20,970] [INFO] Task started: Blastn
[2023-06-05 03:39:20,970] [INFO] Running command: blastn -query GCA_004552005.1_ASM455200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c641246-ace8-4329-b865-c12454f796ca/dqc_reference/reference_markers_gtdb.fasta -out GCA_004552005.1_ASM455200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:39:22,172] [INFO] Task succeeded: Blastn
[2023-06-05 03:39:22,190] [INFO] Selected 10 target genomes.
[2023-06-05 03:39:22,191] [INFO] Target genome list was writen to GCA_004552005.1_ASM455200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:39:22,192] [INFO] Task started: fastANI
[2023-06-05 03:39:22,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa190759-0a29-4a42-865a-772fed58849e/GCA_004552005.1_ASM455200v1_genomic.fna.gz --refList GCA_004552005.1_ASM455200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004552005.1_ASM455200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:39:26,767] [INFO] Task succeeded: fastANI
[2023-06-05 03:39:26,780] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:39:26,781] [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_002404795.1	s__CAG-170 sp002404795	95.6717	434	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	95.77	95.28	0.76	0.71	13	conclusive
GCA_000432135.1	s__CAG-170 sp000432135	85.4474	422	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.47	98.15	0.85	0.82	4	-
GCA_902796245.1	s__CAG-170 sp902796245	84.9784	350	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751035.1	s__CAG-170 sp900751035	84.3296	306	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545925.1	s__CAG-170 sp900545925	83.4988	410	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	98.27	97.70	0.79	0.64	4	-
GCA_002437575.1	s__CAG-170 sp002437575	80.5209	237	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548625.1	s__CAG-170 sp900548625	80.1166	259	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	99.06	98.12	0.91	0.84	3	-
GCA_905214155.1	s__CAG-170 sp905214155	79.6801	225	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803075.1	s__CAG-170 sp902803075	79.5565	205	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549635.1	s__CAG-170 sp900549635	79.0838	230	595	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170	95.0	97.02	95.99	0.80	0.73	4	-
--------------------------------------------------------------------------------
[2023-06-05 03:39:26,783] [INFO] GTDB search result was written to GCA_004552005.1_ASM455200v1_genomic.fna/result_gtdb.tsv
[2023-06-05 03:39:26,783] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:39:26,787] [INFO] DFAST_QC result json was written to GCA_004552005.1_ASM455200v1_genomic.fna/dqc_result.json
[2023-06-05 03:39:26,787] [INFO] DFAST_QC completed!
[2023-06-05 03:39:26,787] [INFO] Total running time: 0h0m50s