[2024-01-24 14:12:34,116] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:34,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:34,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference
[2024-01-24 14:12:35,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:35,437] [INFO] Task started: Prodigal
[2024-01-24 14:12:35,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg14c2b5b9-5cbe-413a-80d6-faf9f752a06c/GCF_000515335.1_ASM51533v1_genomic.fna.gz | prodigal -d GCF_000515335.1_ASM51533v1_genomic.fna/cds.fna -a GCF_000515335.1_ASM51533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:48,767] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:48,768] [INFO] Task started: HMMsearch
[2024-01-24 14:12:48,768] [INFO] Running command: hmmsearch --tblout GCF_000515335.1_ASM51533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference/reference_markers.hmm GCF_000515335.1_ASM51533v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:49,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:49,174] [INFO] Found 6/6 markers.
[2024-01-24 14:12:49,218] [INFO] Query marker FASTA was written to GCF_000515335.1_ASM51533v1_genomic.fna/markers.fasta
[2024-01-24 14:12:49,219] [INFO] Task started: Blastn
[2024-01-24 14:12:49,219] [INFO] Running command: blastn -query GCF_000515335.1_ASM51533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference/reference_markers.fasta -out GCF_000515335.1_ASM51533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:49,876] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:49,880] [INFO] Selected 20 target genomes.
[2024-01-24 14:12:49,880] [INFO] Target genome list was writen to GCF_000515335.1_ASM51533v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:49,897] [INFO] Task started: fastANI
[2024-01-24 14:12:49,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c2b5b9-5cbe-413a-80d6-faf9f752a06c/GCF_000515335.1_ASM51533v1_genomic.fna.gz --refList GCF_000515335.1_ASM51533v1_genomic.fna/target_genomes.txt --output GCF_000515335.1_ASM51533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:10,596] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:10,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:10,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:10,612] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:10,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:10,613] [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 panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	100.0	1589	1590	95	conclusive
Cohnella candidum	strain=18JY8-7	GCA_003713065.1	2674991	2674991	type	True	78.4849	373	1590	95	below_threshold
Cohnella terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	78.4121	378	1590	95	below_threshold
Cohnella cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	78.2816	371	1590	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	78.275	390	1590	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	78.2603	343	1590	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	78.0873	333	1590	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	78.0003	351	1590	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	77.983	360	1590	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	77.9599	388	1590	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	77.9472	348	1590	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	77.9036	326	1590	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_014212015.1	2163172	2163172	type	True	77.8933	318	1590	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	77.771	339	1590	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	77.6733	56	1590	95	below_threshold
Cohnella pontilimi	strain=CAU 1483	GCA_005049045.1	2564100	2564100	type	True	77.6721	265	1590	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.3817	310	1590	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	77.2398	150	1590	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0448	140	1590	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.5954	99	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:10,614] [INFO] DFAST Taxonomy check result was written to GCF_000515335.1_ASM51533v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:10,615] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:10,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:10,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference/checkm_data
[2024-01-24 14:13:10,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:10,666] [INFO] Task started: CheckM
[2024-01-24 14:13:10,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000515335.1_ASM51533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000515335.1_ASM51533v1_genomic.fna/checkm_input GCF_000515335.1_ASM51533v1_genomic.fna/checkm_result
[2024-01-24 14:13:50,638] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:50,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:50,659] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:50,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:50,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000515335.1_ASM51533v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:50,661] [INFO] Task started: Blastn
[2024-01-24 14:13:50,661] [INFO] Running command: blastn -query GCF_000515335.1_ASM51533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aaca787-1133-4afa-8814-43df916f9749/dqc_reference/reference_markers_gtdb.fasta -out GCF_000515335.1_ASM51533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:51,524] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:51,529] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:51,530] [INFO] Target genome list was writen to GCF_000515335.1_ASM51533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:51,589] [INFO] Task started: fastANI
[2024-01-24 14:13:51,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c2b5b9-5cbe-413a-80d6-faf9f752a06c/GCF_000515335.1_ASM51533v1_genomic.fna.gz --refList GCF_000515335.1_ASM51533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000515335.1_ASM51533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:10,016] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:10,030] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:10,030] [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_000515335.1	s__Cohnella panacarvi	100.0	1588	1590	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	78.7479	501	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003713065.1	s__Cohnella candidum	78.4539	369	1590	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	78.4366	476	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007786475.1	s__Cohnella terricola	78.4256	375	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014107495.1	s__Cohnella sp014107495	78.2969	372	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628305.1	s__Cohnella endophytica	78.277	389	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003570905.1	s__Cohnella faecalis	78.2756	340	1590	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	78.2173	395	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990975.1	s__Cohnella sp003990975	78.2119	333	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429825.1	s__Cohnella thermotolerans	78.1332	336	1590	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	78.0062	350	1590	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	77.9795	357	1590	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	77.974	388	1590	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	77.9065	313	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003208555.1	s__Cohnella sp003208555	77.8364	345	1590	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014212055.1	s__Cohnella zeiphila	77.782	337	1590	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 14:14:10,032] [INFO] GTDB search result was written to GCF_000515335.1_ASM51533v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:10,033] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:10,037] [INFO] DFAST_QC result json was written to GCF_000515335.1_ASM51533v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:10,037] [INFO] DFAST_QC completed!
[2024-01-24 14:14:10,037] [INFO] Total running time: 0h1m36s