[2024-01-24 11:05:25,478] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference
[2024-01-24 11:05:26,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,876] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,876] [INFO] Running command: gunzip -c /var/lib/cwl/stgc26d324e-a123-45cb-90c4-acfd3683f962/GCF_007786475.1_ASM778647v1_genomic.fna.gz | prodigal -d GCF_007786475.1_ASM778647v1_genomic.fna/cds.fna -a GCF_007786475.1_ASM778647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:41,183] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:41,184] [INFO] Task started: HMMsearch
[2024-01-24 11:05:41,184] [INFO] Running command: hmmsearch --tblout GCF_007786475.1_ASM778647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference/reference_markers.hmm GCF_007786475.1_ASM778647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:41,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:41,501] [INFO] Found 6/6 markers.
[2024-01-24 11:05:41,544] [INFO] Query marker FASTA was written to GCF_007786475.1_ASM778647v1_genomic.fna/markers.fasta
[2024-01-24 11:05:41,545] [INFO] Task started: Blastn
[2024-01-24 11:05:41,545] [INFO] Running command: blastn -query GCF_007786475.1_ASM778647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference/reference_markers.fasta -out GCF_007786475.1_ASM778647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:42,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:42,164] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:42,164] [INFO] Target genome list was writen to GCF_007786475.1_ASM778647v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:42,169] [INFO] Task started: fastANI
[2024-01-24 11:05:42,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26d324e-a123-45cb-90c4-acfd3683f962/GCF_007786475.1_ASM778647v1_genomic.fna.gz --refList GCF_007786475.1_ASM778647v1_genomic.fna/target_genomes.txt --output GCF_007786475.1_ASM778647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:58,263] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:58,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:58,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:58,276] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:58,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:58,276] [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 terricola	strain=G13	GCA_007786475.1	1289167	1289167	type	True	100.0	1770	1774	95	conclusive
Cohnella cholangitidis	strain=1605-214	GCA_014107495.1	2598458	2598458	type	True	79.4692	550	1774	95	below_threshold
Cohnella herbarum	strain=MFER-1	GCA_012849095.1	2728023	2728023	type	True	79.315	603	1774	95	below_threshold
Cohnella endophytica	strain=M2MS4P-1	GCA_003628305.1	2419778	2419778	type	True	79.1536	571	1774	95	below_threshold
Cohnella luojiensis	strain=CCTCC AB 208254	GCA_004564235.1	652876	652876	type	True	78.9374	438	1774	95	below_threshold
Cohnella lupini	strain=CECT 8236	GCA_003386205.1	1294267	1294267	type	True	78.7501	476	1774	95	below_threshold
Cohnella panacarvi	strain=Gsoil 349	GCA_000515335.1	400776	400776	type	True	78.5399	367	1774	95	below_threshold
Cohnella thermotolerans	strain=DSM 17683	GCA_000429825.1	329858	329858	type	True	77.5519	278	1774	95	below_threshold
Cohnella zeiphila	strain=CBP-2801	GCA_014212055.1	2761120	2761120	type	True	77.4582	315	1774	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.1235	61	1774	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	76.9157	68	1774	95	below_threshold
Paenibacillus mendelii	strain=C/2	GCA_024498075.1	206163	206163	type	True	76.9005	115	1774	95	below_threshold
Thermobacillus composti	strain=KWC4	GCA_000227705.3	377615	377615	type	True	76.7327	132	1774	95	below_threshold
Thermobacillus xylanilyticus	strain=XE	GCA_907165215.1	76633	76633	type	True	76.5778	132	1774	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	76.5315	91	1774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:58,278] [INFO] DFAST Taxonomy check result was written to GCF_007786475.1_ASM778647v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:58,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:58,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:58,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference/checkm_data
[2024-01-24 11:05:58,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:58,330] [INFO] Task started: CheckM
[2024-01-24 11:05:58,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007786475.1_ASM778647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007786475.1_ASM778647v1_genomic.fna/checkm_input GCF_007786475.1_ASM778647v1_genomic.fna/checkm_result
[2024-01-24 11:06:41,572] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:41,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:41,600] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:41,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:41,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007786475.1_ASM778647v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:41,601] [INFO] Task started: Blastn
[2024-01-24 11:06:41,601] [INFO] Running command: blastn -query GCF_007786475.1_ASM778647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb16359d-70e7-4d04-ac10-5e08c7c4341c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007786475.1_ASM778647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:42,400] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:42,403] [INFO] Selected 12 target genomes.
[2024-01-24 11:06:42,403] [INFO] Target genome list was writen to GCF_007786475.1_ASM778647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:42,412] [INFO] Task started: fastANI
[2024-01-24 11:06:42,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgc26d324e-a123-45cb-90c4-acfd3683f962/GCF_007786475.1_ASM778647v1_genomic.fna.gz --refList GCF_007786475.1_ASM778647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007786475.1_ASM778647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:55,777] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:55,793] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:55,794] [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_007786475.1	s__Cohnella terricola	100.0	1770	1774	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_003001675.1	s__Cohnella sp003001675	80.2176	686	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908615.1	s__Cohnella boryungensis	79.6861	584	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386235.1	s__Cohnella phaseoli	79.572	622	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	97.76	97.76	0.83	0.83	2	-
GCF_012849095.1	s__Cohnella sp012849095	79.2966	602	1774	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	79.1545	572	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874175.1	s__Cohnella suwonensis	79.0432	487	1774	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	78.7515	477	1774	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515335.1	s__Cohnella panacarvi	78.5279	371	1774	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 11:06:55,796] [INFO] GTDB search result was written to GCF_007786475.1_ASM778647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:55,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:55,802] [INFO] DFAST_QC result json was written to GCF_007786475.1_ASM778647v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:55,802] [INFO] DFAST_QC completed!
[2024-01-24 11:06:55,802] [INFO] Total running time: 0h1m30s