[2024-01-24 13:22:55,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference
[2024-01-24 13:22:56,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,803] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d7d670e-4f5b-4068-b475-24edb773804c/GCF_002943425.1_ASM294342v1_genomic.fna.gz | prodigal -d GCF_002943425.1_ASM294342v1_genomic.fna/cds.fna -a GCF_002943425.1_ASM294342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:25,653] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:25,653] [INFO] Task started: HMMsearch
[2024-01-24 13:23:25,653] [INFO] Running command: hmmsearch --tblout GCF_002943425.1_ASM294342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference/reference_markers.hmm GCF_002943425.1_ASM294342v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:26,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:26,051] [INFO] Found 6/6 markers.
[2024-01-24 13:23:26,110] [INFO] Query marker FASTA was written to GCF_002943425.1_ASM294342v1_genomic.fna/markers.fasta
[2024-01-24 13:23:26,111] [INFO] Task started: Blastn
[2024-01-24 13:23:26,111] [INFO] Running command: blastn -query GCF_002943425.1_ASM294342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference/reference_markers.fasta -out GCF_002943425.1_ASM294342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:26,718] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:26,722] [INFO] Selected 24 target genomes.
[2024-01-24 13:23:26,722] [INFO] Target genome list was writen to GCF_002943425.1_ASM294342v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:26,745] [INFO] Task started: fastANI
[2024-01-24 13:23:26,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d7d670e-4f5b-4068-b475-24edb773804c/GCF_002943425.1_ASM294342v1_genomic.fna.gz --refList GCF_002943425.1_ASM294342v1_genomic.fna/target_genomes.txt --output GCF_002943425.1_ASM294342v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:51,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:51,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:51,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:51,961] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:51,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:51,962] [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
Siphonobacter curvatus	strain=HR-U	GCA_002943425.1	2094562	2094562	type	True	100.0	2123	2123	95	conclusive
Siphonobacter aquaeclarae	strain=DSM 21668	GCA_900103285.1	563176	563176	type	True	77.1195	311	2123	95	below_threshold
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	75.9223	93	2123	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	75.8753	83	2123	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	75.7745	73	2123	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	75.7457	89	2123	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	75.5975	67	2123	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	75.585	106	2123	95	below_threshold
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	75.5432	85	2123	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	75.5093	97	2123	95	below_threshold
Rhabdobacter roseus	strain=DSM 105074	GCA_014202275.1	1655419	1655419	type	True	75.1321	63	2123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:51,964] [INFO] DFAST Taxonomy check result was written to GCF_002943425.1_ASM294342v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:51,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:51,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:51,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference/checkm_data
[2024-01-24 13:23:51,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:52,032] [INFO] Task started: CheckM
[2024-01-24 13:23:52,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002943425.1_ASM294342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002943425.1_ASM294342v1_genomic.fna/checkm_input GCF_002943425.1_ASM294342v1_genomic.fna/checkm_result
[2024-01-24 13:25:09,629] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:09,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:09,650] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:09,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:09,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002943425.1_ASM294342v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:09,651] [INFO] Task started: Blastn
[2024-01-24 13:25:09,651] [INFO] Running command: blastn -query GCF_002943425.1_ASM294342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf6de33c-cc1d-4d6d-b9d8-076fdd6097c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002943425.1_ASM294342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:10,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:10,460] [INFO] Selected 18 target genomes.
[2024-01-24 13:25:10,461] [INFO] Target genome list was writen to GCF_002943425.1_ASM294342v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:10,548] [INFO] Task started: fastANI
[2024-01-24 13:25:10,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d7d670e-4f5b-4068-b475-24edb773804c/GCF_002943425.1_ASM294342v1_genomic.fna.gz --refList GCF_002943425.1_ASM294342v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002943425.1_ASM294342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:31,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:31,856] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:31,856] [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_002943425.1	s__Siphonobacter curvatus	100.0	2123	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002872335.1	s__Siphonobacter sp002872335	92.7558	1770	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	98.05	98.05	0.92	0.92	2	-
GCF_002838835.1	s__Siphonobacter sp002838835	78.8678	635	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103285.1	s__Siphonobacter aquaeclarae	77.1282	310	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Siphonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003334855.1	s__Larkinella punicea	75.8828	96	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002056795.1	s__Spirosoma aerolatum	75.7745	73	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149005.1	s__Larkinella sp006149005	75.719	90	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	75.5828	68	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727875.1	s__Larkinella sp008727875	75.5753	107	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	75.5025	98	2123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:31,858] [INFO] GTDB search result was written to GCF_002943425.1_ASM294342v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:31,859] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:31,862] [INFO] DFAST_QC result json was written to GCF_002943425.1_ASM294342v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:31,862] [INFO] DFAST_QC completed!
[2024-01-24 13:25:31,862] [INFO] Total running time: 0h2m36s