[2024-01-24 10:57:50,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference
[2024-01-24 10:57:52,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,641] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,641] [INFO] Running command: gunzip -c /var/lib/cwl/stge04fbbdd-8170-480c-b0e6-46a83b54f31b/GCF_003628305.1_ASM362830v1_genomic.fna.gz | prodigal -d GCF_003628305.1_ASM362830v1_genomic.fna/cds.fna -a GCF_003628305.1_ASM362830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:09,022] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:09,023] [INFO] Task started: HMMsearch
[2024-01-24 10:58:09,023] [INFO] Running command: hmmsearch --tblout GCF_003628305.1_ASM362830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference/reference_markers.hmm GCF_003628305.1_ASM362830v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:09,339] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:09,341] [INFO] Found 6/6 markers.
[2024-01-24 10:58:09,405] [INFO] Query marker FASTA was written to GCF_003628305.1_ASM362830v1_genomic.fna/markers.fasta
[2024-01-24 10:58:09,406] [INFO] Task started: Blastn
[2024-01-24 10:58:09,406] [INFO] Running command: blastn -query GCF_003628305.1_ASM362830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference/reference_markers.fasta -out GCF_003628305.1_ASM362830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:09,988] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:09,992] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:09,992] [INFO] Target genome list was writen to GCF_003628305.1_ASM362830v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:09,998] [INFO] Task started: fastANI
[2024-01-24 10:58:09,999] [INFO] Running command: fastANI --query /var/lib/cwl/stge04fbbdd-8170-480c-b0e6-46a83b54f31b/GCF_003628305.1_ASM362830v1_genomic.fna.gz --refList GCF_003628305.1_ASM362830v1_genomic.fna/target_genomes.txt --output GCF_003628305.1_ASM362830v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:24,800] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:24,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:24,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:24,812] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:24,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:24,812] [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
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	100.0	2075	2076	95	conclusive
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	79.916	721	2076	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	79.7297	565	2076	95	below_threshold
Cohnella cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	79.5849	640	2076	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	79.5379	649	2076	95	below_threshold
Cohnella terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	79.2635	556	2076	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	78.1553	392	2076	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	77.1286	328	2076	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	77.0996	65	2076	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	77.0258	231	2076	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	77.018	233	2076	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	76.5186	229	2076	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.3878	91	2076	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.3125	113	2076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:24,814] [INFO] DFAST Taxonomy check result was written to GCF_003628305.1_ASM362830v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:24,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:24,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:24,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference/checkm_data
[2024-01-24 10:58:24,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:24,882] [INFO] Task started: CheckM
[2024-01-24 10:58:24,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003628305.1_ASM362830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003628305.1_ASM362830v1_genomic.fna/checkm_input GCF_003628305.1_ASM362830v1_genomic.fna/checkm_result
[2024-01-24 10:59:13,331] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:13,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:13,356] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:13,357] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:13,357] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003628305.1_ASM362830v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:13,358] [INFO] Task started: Blastn
[2024-01-24 10:59:13,358] [INFO] Running command: blastn -query GCF_003628305.1_ASM362830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00a87a18-f607-421d-814f-a08a9ce0e274/dqc_reference/reference_markers_gtdb.fasta -out GCF_003628305.1_ASM362830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:14,151] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:14,155] [INFO] Selected 9 target genomes.
[2024-01-24 10:59:14,156] [INFO] Target genome list was writen to GCF_003628305.1_ASM362830v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:14,164] [INFO] Task started: fastANI
[2024-01-24 10:59:14,164] [INFO] Running command: fastANI --query /var/lib/cwl/stge04fbbdd-8170-480c-b0e6-46a83b54f31b/GCF_003628305.1_ASM362830v1_genomic.fna.gz --refList GCF_003628305.1_ASM362830v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003628305.1_ASM362830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:26,012] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:26,022] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:26,022] [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_003628305.1	s__Cohnella endophytica	100.0	2075	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017874175.1	s__Cohnella suwonensis	79.9305	687	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849095.1	s__Cohnella sp012849095	79.9141	719	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564235.1	s__Cohnella luojiensis	79.7252	566	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386205.1	s__Cohnella lupini	79.5324	650	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007786475.1	s__Cohnella terricola	79.2703	556	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001675.1	s__Cohnella sp003001675	78.6572	581	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003386235.1	s__Cohnella phaseoli	78.3227	471	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	97.76	97.76	0.83	0.83	2	-
GCF_000515335.1	s__Cohnella panacarvi	78.1489	393	2076	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:26,024] [INFO] GTDB search result was written to GCF_003628305.1_ASM362830v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:26,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:26,028] [INFO] DFAST_QC result json was written to GCF_003628305.1_ASM362830v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:26,028] [INFO] DFAST_QC completed!
[2024-01-24 10:59:26,028] [INFO] Total running time: 0h1m36s