[2024-01-24 13:09:29,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference
[2024-01-24 13:09:30,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,248] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ae868f5-da6a-4007-8257-fdb980a0e263/GCF_007279655.1_ASM727965v1_genomic.fna.gz | prodigal -d GCF_007279655.1_ASM727965v1_genomic.fna/cds.fna -a GCF_007279655.1_ASM727965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:48,379] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:48,379] [INFO] Task started: HMMsearch
[2024-01-24 13:09:48,380] [INFO] Running command: hmmsearch --tblout GCF_007279655.1_ASM727965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference/reference_markers.hmm GCF_007279655.1_ASM727965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:48,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:48,735] [INFO] Found 6/6 markers.
[2024-01-24 13:09:48,775] [INFO] Query marker FASTA was written to GCF_007279655.1_ASM727965v1_genomic.fna/markers.fasta
[2024-01-24 13:09:48,775] [INFO] Task started: Blastn
[2024-01-24 13:09:48,776] [INFO] Running command: blastn -query GCF_007279655.1_ASM727965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference/reference_markers.fasta -out GCF_007279655.1_ASM727965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:49,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:49,398] [INFO] Selected 21 target genomes.
[2024-01-24 13:09:49,399] [INFO] Target genome list was writen to GCF_007279655.1_ASM727965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:49,407] [INFO] Task started: fastANI
[2024-01-24 13:09:49,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae868f5-da6a-4007-8257-fdb980a0e263/GCF_007279655.1_ASM727965v1_genomic.fna.gz --refList GCF_007279655.1_ASM727965v1_genomic.fna/target_genomes.txt --output GCF_007279655.1_ASM727965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:03,553] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:03,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:03,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:03,564] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:03,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:03,565] [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
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	100.0	1455	1457	95	conclusive
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	77.8444	152	1457	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	77.7831	114	1457	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_007279605.1	1227945	1227945	type	True	77.461	166	1457	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_004799345.1	1227945	1227945	type	True	77.4118	163	1457	95	below_threshold
Zhouia spongiae	strain=HN-Y44	GCA_022760175.1	2202721	2202721	type	True	77.1775	90	1457	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.9727	57	1457	95	below_threshold
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	76.8591	103	1457	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.8479	86	1457	95	below_threshold
Sinomicrobium oceani	strain=CGMCC 1.12145	GCA_900119185.1	1150368	1150368	type	True	76.7136	85	1457	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.2614	50	1457	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	76.121	58	1457	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	76.0879	58	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:03,567] [INFO] DFAST Taxonomy check result was written to GCF_007279655.1_ASM727965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:03,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:03,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:03,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference/checkm_data
[2024-01-24 13:10:03,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:03,627] [INFO] Task started: CheckM
[2024-01-24 13:10:03,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007279655.1_ASM727965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007279655.1_ASM727965v1_genomic.fna/checkm_input GCF_007279655.1_ASM727965v1_genomic.fna/checkm_result
[2024-01-24 13:10:59,612] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:59,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:59,641] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:59,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:59,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007279655.1_ASM727965v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:59,642] [INFO] Task started: Blastn
[2024-01-24 13:10:59,642] [INFO] Running command: blastn -query GCF_007279655.1_ASM727965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdcfb4a3-1139-4f60-af8e-1246326418cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_007279655.1_ASM727965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:00,490] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:00,495] [INFO] Selected 23 target genomes.
[2024-01-24 13:11:00,496] [INFO] Target genome list was writen to GCF_007279655.1_ASM727965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:00,540] [INFO] Task started: fastANI
[2024-01-24 13:11:00,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae868f5-da6a-4007-8257-fdb980a0e263/GCF_007279655.1_ASM727965v1_genomic.fna.gz --refList GCF_007279655.1_ASM727965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007279655.1_ASM727965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:14,574] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:14,594] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:14,594] [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_007279655.1	s__Robertkochia solimangrovi	100.0	1455	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013391805.1	s__Galbibacter_A sp013391805	77.9329	100	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016786255.1	s__Robertkochia sp016786255	77.8243	153	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799345.1	s__Robertkochia marina	77.4088	164	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016734785.1	s__Galbibacter_A mesophilus	77.166	105	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	77.0264	65	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116665.1	s__Pustulibacterium marinum	76.9466	56	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pustulibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671605.1	s__Leptobacterium flavescens	76.9044	101	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119185.1	s__Sinomicrobium oceani	76.7136	85	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	76.5729	50	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_000626715.1	s__Aquimarina atlantica	76.1013	56	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846555.1	s__Aquimarina sp002846555	75.7665	50	1457	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:14,596] [INFO] GTDB search result was written to GCF_007279655.1_ASM727965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:14,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:14,600] [INFO] DFAST_QC result json was written to GCF_007279655.1_ASM727965v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:14,600] [INFO] DFAST_QC completed!
[2024-01-24 13:11:14,600] [INFO] Total running time: 0h1m46s