[2024-01-24 14:38:49,866] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:49,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:49,870] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference
[2024-01-24 14:38:52,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:52,373] [INFO] Task started: Prodigal
[2024-01-24 14:38:52,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b1875a4-a441-4e99-90a1-8f76f80b4709/GCF_004365655.1_ASM436565v1_genomic.fna.gz | prodigal -d GCF_004365655.1_ASM436565v1_genomic.fna/cds.fna -a GCF_004365655.1_ASM436565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:09,427] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:09,428] [INFO] Task started: HMMsearch
[2024-01-24 14:39:09,428] [INFO] Running command: hmmsearch --tblout GCF_004365655.1_ASM436565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference/reference_markers.hmm GCF_004365655.1_ASM436565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:09,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:09,718] [INFO] Found 6/6 markers.
[2024-01-24 14:39:09,757] [INFO] Query marker FASTA was written to GCF_004365655.1_ASM436565v1_genomic.fna/markers.fasta
[2024-01-24 14:39:09,758] [INFO] Task started: Blastn
[2024-01-24 14:39:09,758] [INFO] Running command: blastn -query GCF_004365655.1_ASM436565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference/reference_markers.fasta -out GCF_004365655.1_ASM436565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:10,499] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:10,503] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:10,503] [INFO] Target genome list was writen to GCF_004365655.1_ASM436565v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:10,521] [INFO] Task started: fastANI
[2024-01-24 14:39:10,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1875a4-a441-4e99-90a1-8f76f80b4709/GCF_004365655.1_ASM436565v1_genomic.fna.gz --refList GCF_004365655.1_ASM436565v1_genomic.fna/target_genomes.txt --output GCF_004365655.1_ASM436565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:22,263] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:22,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:22,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:22,277] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:22,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:22,278] [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
Epilithonimonas xixisoli	strain=CGMCC 1.12802	GCA_004365655.1	1476462	1476462	type	True	100.0	1123	1123	95	conclusive
Epilithonimonas lactis	strain=LMG 24401	GCA_000735105.1	421072	421072	type	True	85.2035	794	1123	95	below_threshold
Epilithonimonas lactis	strain=DSM 19921	GCA_900110605.1	421072	421072	type	True	85.186	800	1123	95	below_threshold
Epilithonimonas zeae	strain=DSM 27623	GCA_900141765.1	1416779	1416779	type	True	82.8936	754	1123	95	below_threshold
Epilithonimonas tenax	strain=DSM 16811	GCA_000428485.1	191577	191577	type	True	82.7072	689	1123	95	below_threshold
Epilithonimonas hispanica	strain=KCTC 22104	GCA_003385395.1	358687	358687	type	True	82.3018	676	1123	95	below_threshold
Epilithonimonas hungarica	strain=DSM 19684	GCA_900102265.1	454006	454006	type	True	81.8762	683	1123	95	below_threshold
Epilithonimonas arachidiradicis	strain=DSM 27620	GCA_003610695.1	1617282	1617282	type	True	81.5328	703	1123	95	below_threshold
Epilithonimonas arachidiradicis	strain=CCM 8490	GCA_014635405.1	1617282	1617282	type	True	81.498	703	1123	95	below_threshold
Epilithonimonas caeni	strain=DSM 17710	GCA_000426465.1	365343	365343	type	True	81.2005	676	1123	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	78.2572	272	1123	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	77.9307	218	1123	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	77.8209	226	1123	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.1634	158	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:22,279] [INFO] DFAST Taxonomy check result was written to GCF_004365655.1_ASM436565v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:22,280] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:22,280] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:22,280] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference/checkm_data
[2024-01-24 14:39:22,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:22,318] [INFO] Task started: CheckM
[2024-01-24 14:39:22,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365655.1_ASM436565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365655.1_ASM436565v1_genomic.fna/checkm_input GCF_004365655.1_ASM436565v1_genomic.fna/checkm_result
[2024-01-24 14:40:13,120] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:13,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,138] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:13,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:13,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365655.1_ASM436565v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:13,139] [INFO] Task started: Blastn
[2024-01-24 14:40:13,139] [INFO] Running command: blastn -query GCF_004365655.1_ASM436565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2104a3a-6429-4e5f-9a0f-0b637a25de07/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365655.1_ASM436565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:14,173] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:14,176] [INFO] Selected 13 target genomes.
[2024-01-24 14:40:14,177] [INFO] Target genome list was writen to GCF_004365655.1_ASM436565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:14,188] [INFO] Task started: fastANI
[2024-01-24 14:40:14,188] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b1875a4-a441-4e99-90a1-8f76f80b4709/GCF_004365655.1_ASM436565v1_genomic.fna.gz --refList GCF_004365655.1_ASM436565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365655.1_ASM436565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:23,784] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:23,792] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:23,793] [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_004365655.1	s__Epilithonimonas xixisoli	100.0	1123	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017989575.1	s__Epilithonimonas sp017989575	91.0818	582	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735135.1	s__Epilithonimonas sp000735135	86.583	837	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110605.1	s__Epilithonimonas lactis	85.1862	800	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001643375.1	s__Epilithonimonas sp001643375	84.483	762	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000428485.1	s__Epilithonimonas tenax	82.7167	688	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102265.1	s__Epilithonimonas hungarica	81.8919	681	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	97.55	97.55	0.87	0.87	2	-
GCA_002345565.1	s__Epilithonimonas sp002345565	81.4262	614	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248755.1	s__Epilithonimonas sp003248755	81.3359	633	1123	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:23,794] [INFO] GTDB search result was written to GCF_004365655.1_ASM436565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:23,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:23,798] [INFO] DFAST_QC result json was written to GCF_004365655.1_ASM436565v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:23,799] [INFO] DFAST_QC completed!
[2024-01-24 14:40:23,799] [INFO] Total running time: 0h1m34s