[2023-06-08 16:48:13,211] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:48:13,214] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:48:13,215] [INFO] DQC Reference Directory: /var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference
[2023-06-08 16:48:14,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:48:14,515] [INFO] Task started: Prodigal
[2023-06-08 16:48:14,516] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5101163-da62-473e-881c-328313284d72/GCA_945892265.1_MiE-14oct19-101_genomic.fna.gz | prodigal -d GCA_945892265.1_MiE-14oct19-101_genomic.fna/cds.fna -a GCA_945892265.1_MiE-14oct19-101_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:48:38,720] [INFO] Task succeeded: Prodigal
[2023-06-08 16:48:38,721] [INFO] Task started: HMMsearch
[2023-06-08 16:48:38,721] [INFO] Running command: hmmsearch --tblout GCA_945892265.1_MiE-14oct19-101_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference/reference_markers.hmm GCA_945892265.1_MiE-14oct19-101_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:48:38,998] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:48:39,000] [INFO] Found 6/6 markers.
[2023-06-08 16:48:39,040] [INFO] Query marker FASTA was written to GCA_945892265.1_MiE-14oct19-101_genomic.fna/markers.fasta
[2023-06-08 16:48:39,040] [INFO] Task started: Blastn
[2023-06-08 16:48:39,041] [INFO] Running command: blastn -query GCA_945892265.1_MiE-14oct19-101_genomic.fna/markers.fasta -db /var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference/reference_markers.fasta -out GCA_945892265.1_MiE-14oct19-101_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:48:39,628] [INFO] Task succeeded: Blastn
[2023-06-08 16:48:39,632] [INFO] Selected 32 target genomes.
[2023-06-08 16:48:39,632] [INFO] Target genome list was writen to GCA_945892265.1_MiE-14oct19-101_genomic.fna/target_genomes.txt
[2023-06-08 16:48:39,639] [INFO] Task started: fastANI
[2023-06-08 16:48:39,639] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5101163-da62-473e-881c-328313284d72/GCA_945892265.1_MiE-14oct19-101_genomic.fna.gz --refList GCA_945892265.1_MiE-14oct19-101_genomic.fna/target_genomes.txt --output GCA_945892265.1_MiE-14oct19-101_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:48:58,944] [INFO] Task succeeded: fastANI
[2023-06-08 16:48:58,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:48:58,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:48:58,959] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:48:58,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:48:58,959] [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	75.9614	55	1361	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	75.828	60	1361	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	75.8152	81	1361	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.7192	67	1361	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	75.6514	69	1361	95	below_threshold
Trebonia kvetii	strain=15TR583	GCA_007827045.1	2480626	2480626	type	True	74.6913	53	1361	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:48:58,961] [INFO] DFAST Taxonomy check result was written to GCA_945892265.1_MiE-14oct19-101_genomic.fna/tc_result.tsv
[2023-06-08 16:48:58,962] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:48:58,962] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:48:58,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference/checkm_data
[2023-06-08 16:48:58,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:48:59,009] [INFO] Task started: CheckM
[2023-06-08 16:48:59,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945892265.1_MiE-14oct19-101_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945892265.1_MiE-14oct19-101_genomic.fna/checkm_input GCA_945892265.1_MiE-14oct19-101_genomic.fna/checkm_result
[2023-06-08 16:50:05,133] [INFO] Task succeeded: CheckM
[2023-06-08 16:50:05,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:50:05,156] [INFO] ===== Completeness check finished =====
[2023-06-08 16:50:05,157] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:50:05,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945892265.1_MiE-14oct19-101_genomic.fna/markers.fasta)
[2023-06-08 16:50:05,157] [INFO] Task started: Blastn
[2023-06-08 16:50:05,157] [INFO] Running command: blastn -query GCA_945892265.1_MiE-14oct19-101_genomic.fna/markers.fasta -db /var/lib/cwl/stga12c71d5-4e3c-422a-83c5-790fe1266487/dqc_reference/reference_markers_gtdb.fasta -out GCA_945892265.1_MiE-14oct19-101_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:50:05,925] [INFO] Task succeeded: Blastn
[2023-06-08 16:50:05,930] [INFO] Selected 11 target genomes.
[2023-06-08 16:50:05,930] [INFO] Target genome list was writen to GCA_945892265.1_MiE-14oct19-101_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:50:05,936] [INFO] Task started: fastANI
[2023-06-08 16:50:05,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5101163-da62-473e-881c-328313284d72/GCA_945892265.1_MiE-14oct19-101_genomic.fna.gz --refList GCA_945892265.1_MiE-14oct19-101_genomic.fna/target_genomes_gtdb.txt --output GCA_945892265.1_MiE-14oct19-101_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:50:15,038] [INFO] Task succeeded: fastANI
[2023-06-08 16:50:15,050] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 16:50:15,050] [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_002288445.1	s__Arctic95D-9 sp002288445	98.6318	538	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002396885.1	s__Arctic95D-9 sp002396885	84.88	1085	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	82.2518	950	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344525.1	s__Arctic95D-9 sp002344525	79.0237	557	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123695.1	s__Arctic95D-9 sp007123695	78.0367	362	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422425.1	s__Arctic95D-9 sp002422425	77.9375	418	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344215.1	s__Arctic95D-9 sp002344215	77.9206	397	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795505.1	s__JAEUHH01 sp016795505	77.8353	261	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__JAEUHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719225.1	s__Arctic95D-9 sp012719225	77.6344	383	1361	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 16:50:15,052] [INFO] GTDB search result was written to GCA_945892265.1_MiE-14oct19-101_genomic.fna/result_gtdb.tsv
[2023-06-08 16:50:15,053] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:50:15,056] [INFO] DFAST_QC result json was written to GCA_945892265.1_MiE-14oct19-101_genomic.fna/dqc_result.json
[2023-06-08 16:50:15,056] [INFO] DFAST_QC completed!
[2023-06-08 16:50:15,056] [INFO] Total running time: 0h2m2s