[2023-06-29 08:24:17,710] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:24:17,715] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:24:17,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference
[2023-06-29 08:24:20,051] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:24:20,053] [INFO] Task started: Prodigal
[2023-06-29 08:24:20,053] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeb7f89a-d810-4872-ac1f-039db4c5e1d6/GCA_027486655.1_ASM2748665v1_genomic.fna.gz | prodigal -d GCA_027486655.1_ASM2748665v1_genomic.fna/cds.fna -a GCA_027486655.1_ASM2748665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:24:56,464] [INFO] Task succeeded: Prodigal
[2023-06-29 08:24:56,464] [INFO] Task started: HMMsearch
[2023-06-29 08:24:56,464] [INFO] Running command: hmmsearch --tblout GCA_027486655.1_ASM2748665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference/reference_markers.hmm GCA_027486655.1_ASM2748665v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:24:56,763] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:24:56,764] [INFO] Found 6/6 markers.
[2023-06-29 08:24:56,812] [INFO] Query marker FASTA was written to GCA_027486655.1_ASM2748665v1_genomic.fna/markers.fasta
[2023-06-29 08:24:56,813] [INFO] Task started: Blastn
[2023-06-29 08:24:56,813] [INFO] Running command: blastn -query GCA_027486655.1_ASM2748665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference/reference_markers.fasta -out GCA_027486655.1_ASM2748665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:24:57,435] [INFO] Task succeeded: Blastn
[2023-06-29 08:24:57,440] [INFO] Selected 17 target genomes.
[2023-06-29 08:24:57,440] [INFO] Target genome list was writen to GCA_027486655.1_ASM2748665v1_genomic.fna/target_genomes.txt
[2023-06-29 08:24:57,449] [INFO] Task started: fastANI
[2023-06-29 08:24:57,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb7f89a-d810-4872-ac1f-039db4c5e1d6/GCA_027486655.1_ASM2748665v1_genomic.fna.gz --refList GCA_027486655.1_ASM2748665v1_genomic.fna/target_genomes.txt --output GCA_027486655.1_ASM2748665v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:25:11,400] [INFO] Task succeeded: fastANI
[2023-06-29 08:25:11,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:25:11,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:25:11,412] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:25:11,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:25:11,413] [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
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	78.5295	418	1735	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	78.0295	347	1735	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	77.5404	247	1735	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.4041	168	1735	95	below_threshold
Luteolibacter pohnpeiensis	strain=KCTC 22041	GCA_016595435.1	454153	454153	type	True	76.9979	167	1735	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	76.3763	59	1735	95	below_threshold
Akkermansia glycaniphila	strain=Pyt	GCA_001683795.1	1679444	1679444	type	True	76.1981	62	1735	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	75.8354	81	1735	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	75.603	91	1735	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:25:11,414] [INFO] DFAST Taxonomy check result was written to GCA_027486655.1_ASM2748665v1_genomic.fna/tc_result.tsv
[2023-06-29 08:25:11,415] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:25:11,415] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:25:11,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference/checkm_data
[2023-06-29 08:25:11,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:25:11,467] [INFO] Task started: CheckM
[2023-06-29 08:25:11,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027486655.1_ASM2748665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027486655.1_ASM2748665v1_genomic.fna/checkm_input GCA_027486655.1_ASM2748665v1_genomic.fna/checkm_result
[2023-06-29 08:26:57,203] [INFO] Task succeeded: CheckM
[2023-06-29 08:26:57,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:26:57,227] [INFO] ===== Completeness check finished =====
[2023-06-29 08:26:57,228] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:26:57,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027486655.1_ASM2748665v1_genomic.fna/markers.fasta)
[2023-06-29 08:26:57,228] [INFO] Task started: Blastn
[2023-06-29 08:26:57,229] [INFO] Running command: blastn -query GCA_027486655.1_ASM2748665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36021c27-0f3a-48e7-b61b-7a1cd84d40eb/dqc_reference/reference_markers_gtdb.fasta -out GCA_027486655.1_ASM2748665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:26:58,072] [INFO] Task succeeded: Blastn
[2023-06-29 08:26:58,076] [INFO] Selected 19 target genomes.
[2023-06-29 08:26:58,076] [INFO] Target genome list was writen to GCA_027486655.1_ASM2748665v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:26:58,097] [INFO] Task started: fastANI
[2023-06-29 08:26:58,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb7f89a-d810-4872-ac1f-039db4c5e1d6/GCA_027486655.1_ASM2748665v1_genomic.fna.gz --refList GCA_027486655.1_ASM2748665v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027486655.1_ASM2748665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:27:11,783] [INFO] Task succeeded: fastANI
[2023-06-29 08:27:11,804] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:27:11,804] [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
GCA_003820635.1	s__Luteolibacter sp003820635	80.3052	447	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919975.1	s__Luteolibacter sp903919975	78.6575	377	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCA_903909905.1	s__Luteolibacter sp903909905	78.5654	183	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969605.1	s__Luteolibacter sp018969605	78.5562	246	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595465.1	s__Luteolibacter yonseiensis	78.5284	418	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906515.1	s__Luteolibacter sp903906515	78.5061	373	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.85	99.81	0.93	0.92	3	-
GCA_018402445.1	s__Luteolibacter sp018402445	78.0279	258	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904755.1	s__Haloferula sp014904755	78.0207	295	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	78.0095	349	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888515.1	s__Luteolibacter sp903888515	77.9619	309	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.90	0.94	0.94	2	-
GCA_005787565.1	s__Luteolibacter sp005787565	77.9191	275	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126655.1	s__Luteolibacter sp007126655	77.9091	282	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.62	99.62	0.82	0.82	2	-
GCA_017798145.1	s__Luteolibacter sp017798145	77.8729	297	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871685.1	s__Luteolibacter sp016871685	77.8415	220	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301995.1	s__Luteolibacter sp017301995	77.821	404	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934285.1	s__Luteolibacter sp903934285	77.5347	269	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.86	99.86	0.92	0.92	3	-
GCA_903826205.1	s__Luteolibacter sp903826205	77.4142	258	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.67	99.65	0.89	0.88	3	-
GCA_903837825.1	s__Luteolibacter sp903837825	77.1616	131	1735	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:27:11,806] [INFO] GTDB search result was written to GCA_027486655.1_ASM2748665v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:27:11,807] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:27:11,811] [INFO] DFAST_QC result json was written to GCA_027486655.1_ASM2748665v1_genomic.fna/dqc_result.json
[2023-06-29 08:27:11,811] [INFO] DFAST_QC completed!
[2023-06-29 08:27:11,812] [INFO] Total running time: 0h2m54s