[2024-01-25 18:13:20,742] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:20,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:20,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference
[2024-01-25 18:13:21,889] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:21,890] [INFO] Task started: Prodigal
[2024-01-25 18:13:21,890] [INFO] Running command: gunzip -c /var/lib/cwl/stg087ccb09-8382-4dd5-83d7-1b3dbac59c08/GCF_900169535.1_PRJEB19972_genomic.fna.gz | prodigal -d GCF_900169535.1_PRJEB19972_genomic.fna/cds.fna -a GCF_900169535.1_PRJEB19972_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:37,506] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:37,506] [INFO] Task started: HMMsearch
[2024-01-25 18:13:37,506] [INFO] Running command: hmmsearch --tblout GCF_900169535.1_PRJEB19972_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference/reference_markers.hmm GCF_900169535.1_PRJEB19972_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:37,935] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:37,936] [INFO] Found 6/6 markers.
[2024-01-25 18:13:37,995] [INFO] Query marker FASTA was written to GCF_900169535.1_PRJEB19972_genomic.fna/markers.fasta
[2024-01-25 18:13:37,996] [INFO] Task started: Blastn
[2024-01-25 18:13:37,996] [INFO] Running command: blastn -query GCF_900169535.1_PRJEB19972_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference/reference_markers.fasta -out GCF_900169535.1_PRJEB19972_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:38,620] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:38,623] [INFO] Selected 16 target genomes.
[2024-01-25 18:13:38,624] [INFO] Target genome list was writen to GCF_900169535.1_PRJEB19972_genomic.fna/target_genomes.txt
[2024-01-25 18:13:38,636] [INFO] Task started: fastANI
[2024-01-25 18:13:38,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg087ccb09-8382-4dd5-83d7-1b3dbac59c08/GCF_900169535.1_PRJEB19972_genomic.fna.gz --refList GCF_900169535.1_PRJEB19972_genomic.fna/target_genomes.txt --output GCF_900169535.1_PRJEB19972_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:55,986] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:55,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:55,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:55,997] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:55,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:55,998] [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 laeviribosi	strain=DSM 21336	GCA_000378425.1	380174	380174	type	True	81.0402	770	2102	95	below_threshold
Cohnella xylanilytica	strain=DSM 25239	GCA_014212175.1	557555	557555	type	True	79.5441	649	2102	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	79.5111	579	2102	95	below_threshold
Cohnella lubricantis	strain=DSM 103658	GCA_017874835.1	2163172	2163172	type	True	79.1446	409	2102	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	78.6894	535	2102	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	78.6325	466	2102	95	below_threshold
Cohnella fermenti	strain=CC-MHH1044	GCA_004801405.1	2565925	2565925	type	True	78.4147	462	2102	95	below_threshold
Paenibacillus flagellatus	strain=DXL2	GCA_003217775.1	2211139	2211139	type	True	78.1491	367	2102	95	below_threshold
Cohnella faecalis	strain=K2E09-144	GCA_003570905.1	2315694	2315694	type	True	77.9383	297	2102	95	below_threshold
Paenibacillus albicereus	strain=UniB2	GCA_012676905.1	2726185	2726185	type	True	77.5003	295	2102	95	below_threshold
Paenibacillus artemisiicola	strain=MWE-103	GCA_017652985.1	1172618	1172618	type	True	77.257	367	2102	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.1715	161	2102	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.1096	79	2102	95	below_threshold
Paenibacillus montanisoli	strain=RA17	GCA_003268025.1	2081970	2081970	type	True	76.3562	172	2102	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.351	105	2102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:55,999] [INFO] DFAST Taxonomy check result was written to GCF_900169535.1_PRJEB19972_genomic.fna/tc_result.tsv
[2024-01-25 18:13:56,000] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:56,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:56,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference/checkm_data
[2024-01-25 18:13:56,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:56,063] [INFO] Task started: CheckM
[2024-01-25 18:13:56,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900169535.1_PRJEB19972_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900169535.1_PRJEB19972_genomic.fna/checkm_input GCF_900169535.1_PRJEB19972_genomic.fna/checkm_result
[2024-01-25 18:14:39,494] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:39,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:39,515] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:39,515] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:39,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900169535.1_PRJEB19972_genomic.fna/markers.fasta)
[2024-01-25 18:14:39,516] [INFO] Task started: Blastn
[2024-01-25 18:14:39,516] [INFO] Running command: blastn -query GCF_900169535.1_PRJEB19972_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a44a35b-6c5a-47c9-836c-39569c7eb698/dqc_reference/reference_markers_gtdb.fasta -out GCF_900169535.1_PRJEB19972_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:40,433] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:40,437] [INFO] Selected 12 target genomes.
[2024-01-25 18:14:40,437] [INFO] Target genome list was writen to GCF_900169535.1_PRJEB19972_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:40,466] [INFO] Task started: fastANI
[2024-01-25 18:14:40,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg087ccb09-8382-4dd5-83d7-1b3dbac59c08/GCF_900169535.1_PRJEB19972_genomic.fna.gz --refList GCF_900169535.1_PRJEB19972_genomic.fna/target_genomes_gtdb.txt --output GCF_900169535.1_PRJEB19972_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:56,467] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:56,476] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:56,476] [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_016937515.1	s__Cohnella algarum	99.0485	1812	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.08	99.08	0.87	0.87	3	conclusive
GCF_000378425.1	s__Cohnella laeviribosi	81.0427	771	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.97	98.97	0.91	0.91	2	-
GCF_014212175.1	s__Cohnella xylanilytica	79.5648	648	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	98.90	98.90	0.93	0.93	2	-
GCF_000429825.1	s__Cohnella thermotolerans	79.5503	575	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212015.1	s__Cohnella lubricantis	79.2034	401	2102	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	78.6714	539	2102	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	78.6333	466	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801405.1	s__Cohnella sp004801405	78.4307	459	2102	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	78.117	392	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091135.1	s__Cohnella sp019091135	78.0218	456	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208555.1	s__Cohnella sp003208555	77.9956	466	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017874175.1	s__Cohnella suwonensis	77.775	352	2102	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:56,477] [INFO] GTDB search result was written to GCF_900169535.1_PRJEB19972_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:56,478] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:56,481] [INFO] DFAST_QC result json was written to GCF_900169535.1_PRJEB19972_genomic.fna/dqc_result.json
[2024-01-25 18:14:56,481] [INFO] DFAST_QC completed!
[2024-01-25 18:14:56,481] [INFO] Total running time: 0h1m36s