[2024-01-24 13:17:14,055] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference
[2024-01-24 13:17:15,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,354] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,355] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8983e83-2906-4bb2-b249-8186791f24c2/GCF_003602095.1_ASM360209v1_genomic.fna.gz | prodigal -d GCF_003602095.1_ASM360209v1_genomic.fna/cds.fna -a GCF_003602095.1_ASM360209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:29,752] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:29,753] [INFO] Task started: HMMsearch
[2024-01-24 13:17:29,753] [INFO] Running command: hmmsearch --tblout GCF_003602095.1_ASM360209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference/reference_markers.hmm GCF_003602095.1_ASM360209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:30,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:30,128] [INFO] Found 6/6 markers.
[2024-01-24 13:17:30,175] [INFO] Query marker FASTA was written to GCF_003602095.1_ASM360209v1_genomic.fna/markers.fasta
[2024-01-24 13:17:30,176] [INFO] Task started: Blastn
[2024-01-24 13:17:30,176] [INFO] Running command: blastn -query GCF_003602095.1_ASM360209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference/reference_markers.fasta -out GCF_003602095.1_ASM360209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:31,060] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:31,064] [INFO] Selected 10 target genomes.
[2024-01-24 13:17:31,065] [INFO] Target genome list was writen to GCF_003602095.1_ASM360209v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:31,104] [INFO] Task started: fastANI
[2024-01-24 13:17:31,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8983e83-2906-4bb2-b249-8186791f24c2/GCF_003602095.1_ASM360209v1_genomic.fna.gz --refList GCF_003602095.1_ASM360209v1_genomic.fna/target_genomes.txt --output GCF_003602095.1_ASM360209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:44,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:44,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:44,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:44,296] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:44,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:44,296] [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
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	100.0	1769	1771	95	conclusive
Rahnella bruchi	strain=DSM 27398	GCA_003614975.1	1510573	1510573	type	True	93.6014	1492	1771	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	92.4807	1492	1771	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003602185.1	574964	574964	type	True	91.1958	1374	1771	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003610915.1	574964	574964	type	True	91.1346	1396	1771	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	91.0226	1404	1771	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	88.2237	1345	1771	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	86.9864	1154	1771	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	86.1751	1292	1771	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.2057	596	1771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:44,298] [INFO] DFAST Taxonomy check result was written to GCF_003602095.1_ASM360209v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:44,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:44,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:44,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference/checkm_data
[2024-01-24 13:17:44,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:44,357] [INFO] Task started: CheckM
[2024-01-24 13:17:44,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003602095.1_ASM360209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003602095.1_ASM360209v1_genomic.fna/checkm_input GCF_003602095.1_ASM360209v1_genomic.fna/checkm_result
[2024-01-24 13:18:30,671] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:30,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:30,701] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:30,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:30,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003602095.1_ASM360209v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:30,702] [INFO] Task started: Blastn
[2024-01-24 13:18:30,702] [INFO] Running command: blastn -query GCF_003602095.1_ASM360209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74ae9543-490a-4703-9d26-cfe3c5e5069c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003602095.1_ASM360209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:31,881] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:31,885] [INFO] Selected 6 target genomes.
[2024-01-24 13:18:31,886] [INFO] Target genome list was writen to GCF_003602095.1_ASM360209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:31,895] [INFO] Task started: fastANI
[2024-01-24 13:18:31,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8983e83-2906-4bb2-b249-8186791f24c2/GCF_003602095.1_ASM360209v1_genomic.fna.gz --refList GCF_003602095.1_ASM360209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003602095.1_ASM360209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:40,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:40,517] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:40,517] [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_003602095.1	s__Rahnella woolbedingensis	100.0	1769	1771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003614975.1	s__Rahnella bruchi	93.6014	1492	1771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049625.1	s__Rahnella sp019049625	92.4807	1492	1771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610915.1	s__Rahnella variigena	91.1543	1394	1771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_019049675.1	s__Rahnella sp019049675	91.0226	1404	1771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004330295.1	s__Rahnella victoriana	88.2238	1344	1771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:40,519] [INFO] GTDB search result was written to GCF_003602095.1_ASM360209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:40,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:40,523] [INFO] DFAST_QC result json was written to GCF_003602095.1_ASM360209v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:40,523] [INFO] DFAST_QC completed!
[2024-01-24 13:18:40,523] [INFO] Total running time: 0h1m26s