[2024-01-24 10:47:06,592] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference
[2024-01-24 10:47:12,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,799] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,800] [INFO] Running command: gunzip -c /var/lib/cwl/stgafd4a235-08d4-46fe-b912-7f646ac7fc37/GCF_007992435.1_ASM799243v1_genomic.fna.gz | prodigal -d GCF_007992435.1_ASM799243v1_genomic.fna/cds.fna -a GCF_007992435.1_ASM799243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:12,135] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:12,136] [INFO] Task started: HMMsearch
[2024-01-24 10:48:12,136] [INFO] Running command: hmmsearch --tblout GCF_007992435.1_ASM799243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference/reference_markers.hmm GCF_007992435.1_ASM799243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:12,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:12,508] [INFO] Found 6/6 markers.
[2024-01-24 10:48:12,566] [INFO] Query marker FASTA was written to GCF_007992435.1_ASM799243v1_genomic.fna/markers.fasta
[2024-01-24 10:48:12,566] [INFO] Task started: Blastn
[2024-01-24 10:48:12,566] [INFO] Running command: blastn -query GCF_007992435.1_ASM799243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference/reference_markers.fasta -out GCF_007992435.1_ASM799243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:13,195] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:13,198] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:13,199] [INFO] Target genome list was writen to GCF_007992435.1_ASM799243v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:13,219] [INFO] Task started: fastANI
[2024-01-24 10:48:13,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgafd4a235-08d4-46fe-b912-7f646ac7fc37/GCF_007992435.1_ASM799243v1_genomic.fna.gz --refList GCF_007992435.1_ASM799243v1_genomic.fna/target_genomes.txt --output GCF_007992435.1_ASM799243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:31,014] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:31,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:31,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:31,031] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:31,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:31,031] [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
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	100.0	2478	2486	95	conclusive
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	77.9319	589	2486	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	77.6491	441	2486	95	below_threshold
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	77.4385	455	2486	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	77.3568	457	2486	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	76.8085	312	2486	95	below_threshold
Verrucomicrobium spinosum	strain=JCM 18804	GCA_001313125.1	2736	2736	type	True	76.6372	266	2486	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.59	278	2486	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	76.1864	95	2486	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.0114	121	2486	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	75.9695	65	2486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:31,033] [INFO] DFAST Taxonomy check result was written to GCF_007992435.1_ASM799243v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:31,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:31,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:31,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference/checkm_data
[2024-01-24 10:48:31,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:31,101] [INFO] Task started: CheckM
[2024-01-24 10:48:31,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992435.1_ASM799243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992435.1_ASM799243v1_genomic.fna/checkm_input GCF_007992435.1_ASM799243v1_genomic.fna/checkm_result
[2024-01-24 10:51:16,682] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:16,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:16,714] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:16,714] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:16,715] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992435.1_ASM799243v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:16,715] [INFO] Task started: Blastn
[2024-01-24 10:51:16,715] [INFO] Running command: blastn -query GCF_007992435.1_ASM799243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73631bba-b741-4d54-afce-29ac42bec146/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992435.1_ASM799243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:17,658] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:17,662] [INFO] Selected 18 target genomes.
[2024-01-24 10:51:17,663] [INFO] Target genome list was writen to GCF_007992435.1_ASM799243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:17,678] [INFO] Task started: fastANI
[2024-01-24 10:51:17,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgafd4a235-08d4-46fe-b912-7f646ac7fc37/GCF_007992435.1_ASM799243v1_genomic.fna.gz --refList GCF_007992435.1_ASM799243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992435.1_ASM799243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:39,380] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:39,397] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:39,397] [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_007992435.1	s__Prosthecobacter gellanilyticus	100.0	2478	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019186985.1	s__Prosthecobacter sp019186985	78.9654	837	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336895.1	s__Prosthecobacter sp002336895	78.0557	627	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795465.1	s__Prosthecobacter sp016795465	78.0343	641	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879935.1	s__Prosthecobacter sp014879935	77.9829	623	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203095.1	s__Prosthecobacter vanneervenii	77.9599	582	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301975.1	s__Prosthecobacter sp017301975	77.894	597	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848465.1	s__Prosthecobacter sp903848465	77.8478	507	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.97	99.92	0.97	0.96	6	-
GCA_015075365.1	s__Prosthecobacter sp015075365	77.7981	680	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343505.1	s__Prosthecobacter sp002343505	77.7885	573	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	98.23	97.36	0.90	0.88	4	-
GCA_002482965.1	s__Prosthecobacter sp002482965	77.7781	575	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960845.1	s__Prosthecobacter sp903960845	77.7402	519	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.18	98.90	0.84	0.82	4	-
GCF_900167535.1	s__Prosthecobacter debontii	77.6505	440	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279765.1	s__Prosthecobacter sp002279765	77.5984	525	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203045.1	s__Prosthecobacter dejongeii	77.4539	454	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364345.1	s__Prosthecobacter fusiformis	77.3509	458	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453085.1	s__Prosthecobacter sp003453085	77.3223	320	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903854655.1	s__CAINXC01 sp903854655	76.4497	305	2486	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__CAINXC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:39,399] [INFO] GTDB search result was written to GCF_007992435.1_ASM799243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:39,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:39,403] [INFO] DFAST_QC result json was written to GCF_007992435.1_ASM799243v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:39,403] [INFO] DFAST_QC completed!
[2024-01-24 10:51:39,403] [INFO] Total running time: 0h4m33s