[2024-01-24 14:15:01,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:01,115] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:01,116] [INFO] DQC Reference Directory: /var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference
[2024-01-24 14:15:02,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:02,542] [INFO] Task started: Prodigal
[2024-01-24 14:15:02,542] [INFO] Running command: gunzip -c /var/lib/cwl/stgc98c11d0-86be-425c-863c-c93259788fde/GCF_004801405.1_ASM480140v1_genomic.fna.gz | prodigal -d GCF_004801405.1_ASM480140v1_genomic.fna/cds.fna -a GCF_004801405.1_ASM480140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:26,339] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:26,339] [INFO] Task started: HMMsearch
[2024-01-24 14:15:26,339] [INFO] Running command: hmmsearch --tblout GCF_004801405.1_ASM480140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference/reference_markers.hmm GCF_004801405.1_ASM480140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:26,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:26,741] [INFO] Found 6/6 markers.
[2024-01-24 14:15:26,807] [INFO] Query marker FASTA was written to GCF_004801405.1_ASM480140v1_genomic.fna/markers.fasta
[2024-01-24 14:15:26,807] [INFO] Task started: Blastn
[2024-01-24 14:15:26,807] [INFO] Running command: blastn -query GCF_004801405.1_ASM480140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference/reference_markers.fasta -out GCF_004801405.1_ASM480140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:27,485] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:27,492] [INFO] Selected 13 target genomes.
[2024-01-24 14:15:27,492] [INFO] Target genome list was writen to GCF_004801405.1_ASM480140v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:27,498] [INFO] Task started: fastANI
[2024-01-24 14:15:27,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgc98c11d0-86be-425c-863c-c93259788fde/GCF_004801405.1_ASM480140v1_genomic.fna.gz --refList GCF_004801405.1_ASM480140v1_genomic.fna/target_genomes.txt --output GCF_004801405.1_ASM480140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:44,612] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:44,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:44,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:44,629] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:44,629] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:44,630] [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 fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	100.0	2775	2781	95	conclusive
Cohnella thailandensis	strain=DSM 25241	GCA_017874075.1	557557	557557	type	True	82.4696	1220	2781	95	below_threshold
Cohnella thailandensis	strain=DSM 25241	GCA_014212135.1	557557	557557	type	True	82.4173	1228	2781	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	80.0862	863	2781	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	79.305	556	2781	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	79.3047	561	2781	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	79.1104	693	2781	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	78.9984	627	2781	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.6546	403	2781	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.2084	451	2781	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.8209	185	2781	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.6371	205	2781	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	75.9329	198	2781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:44,631] [INFO] DFAST Taxonomy check result was written to GCF_004801405.1_ASM480140v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:44,632] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:44,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:44,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference/checkm_data
[2024-01-24 14:15:44,633] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:44,712] [INFO] Task started: CheckM
[2024-01-24 14:15:44,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801405.1_ASM480140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801405.1_ASM480140v1_genomic.fna/checkm_input GCF_004801405.1_ASM480140v1_genomic.fna/checkm_result
[2024-01-24 14:16:49,586] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:49,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:49,609] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:49,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:49,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801405.1_ASM480140v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:49,610] [INFO] Task started: Blastn
[2024-01-24 14:16:49,611] [INFO] Running command: blastn -query GCF_004801405.1_ASM480140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec4b8578-b81e-41f5-a95c-eedd4658cbee/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801405.1_ASM480140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:50,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:50,670] [INFO] Selected 7 target genomes.
[2024-01-24 14:16:50,670] [INFO] Target genome list was writen to GCF_004801405.1_ASM480140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:50,682] [INFO] Task started: fastANI
[2024-01-24 14:16:50,683] [INFO] Running command: fastANI --query /var/lib/cwl/stgc98c11d0-86be-425c-863c-c93259788fde/GCF_004801405.1_ASM480140v1_genomic.fna.gz --refList GCF_004801405.1_ASM480140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801405.1_ASM480140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:03,933] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:03,946] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:03,947] [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_004801405.1	s__Cohnella sp004801405	100.0	2775	2781	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_014212135.1	s__Cohnella thailandensis	82.4231	1226	2781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003990975.1	s__Cohnella sp003990975	81.3848	996	2781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212175.1	s__Cohnella xylanilytica	80.0782	867	2781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_014212015.1	s__Cohnella lubricantis	79.3061	556	2781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014212055.1	s__Cohnella zeiphila	79.0998	694	2781	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212125.1	s__Cohnella nanjingensis	78.9971	627	2781	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 14:17:03,948] [INFO] GTDB search result was written to GCF_004801405.1_ASM480140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:03,949] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:03,953] [INFO] DFAST_QC result json was written to GCF_004801405.1_ASM480140v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:03,954] [INFO] DFAST_QC completed!
[2024-01-24 14:17:03,954] [INFO] Total running time: 0h2m3s