[2024-01-25 19:59:50,798] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:50,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:50,801] [INFO] DQC Reference Directory: /var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference
[2024-01-25 19:59:51,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:51,941] [INFO] Task started: Prodigal
[2024-01-25 19:59:51,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg9807e1f8-c09e-4f4b-9a99-7d702704d930/GCF_016595435.1_ASM1659543v1_genomic.fna.gz | prodigal -d GCF_016595435.1_ASM1659543v1_genomic.fna/cds.fna -a GCF_016595435.1_ASM1659543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:15,490] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:15,490] [INFO] Task started: HMMsearch
[2024-01-25 20:00:15,490] [INFO] Running command: hmmsearch --tblout GCF_016595435.1_ASM1659543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference/reference_markers.hmm GCF_016595435.1_ASM1659543v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:15,714] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:15,715] [INFO] Found 6/6 markers.
[2024-01-25 20:00:15,752] [INFO] Query marker FASTA was written to GCF_016595435.1_ASM1659543v1_genomic.fna/markers.fasta
[2024-01-25 20:00:15,753] [INFO] Task started: Blastn
[2024-01-25 20:00:15,753] [INFO] Running command: blastn -query GCF_016595435.1_ASM1659543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference/reference_markers.fasta -out GCF_016595435.1_ASM1659543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:16,282] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:16,287] [INFO] Selected 13 target genomes.
[2024-01-25 20:00:16,287] [INFO] Target genome list was writen to GCF_016595435.1_ASM1659543v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:16,296] [INFO] Task started: fastANI
[2024-01-25 20:00:16,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg9807e1f8-c09e-4f4b-9a99-7d702704d930/GCF_016595435.1_ASM1659543v1_genomic.fna.gz --refList GCF_016595435.1_ASM1659543v1_genomic.fna/target_genomes.txt --output GCF_016595435.1_ASM1659543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:26,209] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:26,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:26,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:26,216] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:26,216] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:26,216] [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 pohnpeiensis	strain=KCTC 22041	GCA_016595435.1	454153	454153	type	True	100.0	1459	1467	95	conclusive
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	77.2254	188	1467	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.9987	105	1467	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	76.7909	68	1467	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.6738	165	1467	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.56	68	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:26,217] [INFO] DFAST Taxonomy check result was written to GCF_016595435.1_ASM1659543v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:26,218] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:26,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:26,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference/checkm_data
[2024-01-25 20:00:26,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:26,267] [INFO] Task started: CheckM
[2024-01-25 20:00:26,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595435.1_ASM1659543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595435.1_ASM1659543v1_genomic.fna/checkm_input GCF_016595435.1_ASM1659543v1_genomic.fna/checkm_result
[2024-01-25 20:01:32,380] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:32,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:32,402] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:32,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:32,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595435.1_ASM1659543v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:32,403] [INFO] Task started: Blastn
[2024-01-25 20:01:32,403] [INFO] Running command: blastn -query GCF_016595435.1_ASM1659543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga94ee1c0-70f7-44f2-89a9-8f6f1c7408fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595435.1_ASM1659543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:33,258] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:33,269] [INFO] Selected 19 target genomes.
[2024-01-25 20:01:33,269] [INFO] Target genome list was writen to GCF_016595435.1_ASM1659543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:33,331] [INFO] Task started: fastANI
[2024-01-25 20:01:33,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg9807e1f8-c09e-4f4b-9a99-7d702704d930/GCF_016595435.1_ASM1659543v1_genomic.fna.gz --refList GCF_016595435.1_ASM1659543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595435.1_ASM1659543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:48,754] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:48,767] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:48,767] [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_016595435.1	s__Luteolibacter pohnpeiensis	100.0	1459	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002307065.1	s__Luteolibacter sp002307065	77.53	187	1467	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	77.2108	189	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	77.1842	129	1467	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	77.1437	139	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCA_903837825.1	s__Luteolibacter sp903837825	76.9825	85	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	76.9748	106	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969605.1	s__Luteolibacter sp018969605	76.9446	102	1467	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	76.8598	124	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301995.1	s__Luteolibacter sp017301995	76.6978	116	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	76.6603	166	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	76.6558	122	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032235.1	s__Luteolibacter sp012032235	76.6555	85	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	76.5204	86	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908495.1	s__Luteolibacter sp903908495	76.4634	114	1467	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	76.4054	95	1467	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	76.3344	96	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.67	99.65	0.89	0.88	3	-
GCA_007126655.1	s__Luteolibacter sp007126655	76.215	93	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.62	99.62	0.82	0.82	2	-
GCA_903875675.1	s__Luteolibacter sp903875675	76.1052	64	1467	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:48,769] [INFO] GTDB search result was written to GCF_016595435.1_ASM1659543v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:48,769] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:48,772] [INFO] DFAST_QC result json was written to GCF_016595435.1_ASM1659543v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:48,772] [INFO] DFAST_QC completed!
[2024-01-25 20:01:48,772] [INFO] Total running time: 0h1m58s