[2024-01-25 17:58:35,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:58:35,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:58:35,632] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference
[2024-01-25 17:58:36,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:58:36,864] [INFO] Task started: Prodigal
[2024-01-25 17:58:36,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg4db46844-f870-44ad-bdd2-bb44837c2d9d/GCF_020782115.1_ASM2078211v1_genomic.fna.gz | prodigal -d GCF_020782115.1_ASM2078211v1_genomic.fna/cds.fna -a GCF_020782115.1_ASM2078211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:58:51,357] [INFO] Task succeeded: Prodigal
[2024-01-25 17:58:51,358] [INFO] Task started: HMMsearch
[2024-01-25 17:58:51,358] [INFO] Running command: hmmsearch --tblout GCF_020782115.1_ASM2078211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference/reference_markers.hmm GCF_020782115.1_ASM2078211v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:58:51,609] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:58:51,610] [INFO] Found 6/6 markers.
[2024-01-25 17:58:51,649] [INFO] Query marker FASTA was written to GCF_020782115.1_ASM2078211v1_genomic.fna/markers.fasta
[2024-01-25 17:58:51,649] [INFO] Task started: Blastn
[2024-01-25 17:58:51,649] [INFO] Running command: blastn -query GCF_020782115.1_ASM2078211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference/reference_markers.fasta -out GCF_020782115.1_ASM2078211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:58:52,238] [INFO] Task succeeded: Blastn
[2024-01-25 17:58:52,241] [INFO] Selected 13 target genomes.
[2024-01-25 17:58:52,241] [INFO] Target genome list was writen to GCF_020782115.1_ASM2078211v1_genomic.fna/target_genomes.txt
[2024-01-25 17:58:52,249] [INFO] Task started: fastANI
[2024-01-25 17:58:52,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg4db46844-f870-44ad-bdd2-bb44837c2d9d/GCF_020782115.1_ASM2078211v1_genomic.fna.gz --refList GCF_020782115.1_ASM2078211v1_genomic.fna/target_genomes.txt --output GCF_020782115.1_ASM2078211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:59:01,630] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:01,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:59:01,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:59:01,638] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:59:01,638] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:59:01,639] [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
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	89.297	1134	1442	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	79.081	494	1442	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	78.8961	475	1442	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	78.8836	557	1442	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	78.8201	497	1442	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	78.813	499	1442	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.5268	492	1442	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.6452	55	1442	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.1038	91	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:59:01,640] [INFO] DFAST Taxonomy check result was written to GCF_020782115.1_ASM2078211v1_genomic.fna/tc_result.tsv
[2024-01-25 17:59:01,640] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:59:01,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:59:01,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference/checkm_data
[2024-01-25 17:59:01,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:59:01,682] [INFO] Task started: CheckM
[2024-01-25 17:59:01,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020782115.1_ASM2078211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020782115.1_ASM2078211v1_genomic.fna/checkm_input GCF_020782115.1_ASM2078211v1_genomic.fna/checkm_result
[2024-01-25 17:59:44,773] [INFO] Task succeeded: CheckM
[2024-01-25 17:59:44,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:59:44,790] [INFO] ===== Completeness check finished =====
[2024-01-25 17:59:44,791] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:59:44,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020782115.1_ASM2078211v1_genomic.fna/markers.fasta)
[2024-01-25 17:59:44,792] [INFO] Task started: Blastn
[2024-01-25 17:59:44,792] [INFO] Running command: blastn -query GCF_020782115.1_ASM2078211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a4f98a-3be6-4c58-bd65-fde6e62365d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_020782115.1_ASM2078211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:59:45,689] [INFO] Task succeeded: Blastn
[2024-01-25 17:59:45,692] [INFO] Selected 11 target genomes.
[2024-01-25 17:59:45,692] [INFO] Target genome list was writen to GCF_020782115.1_ASM2078211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:59:45,700] [INFO] Task started: fastANI
[2024-01-25 17:59:45,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg4db46844-f870-44ad-bdd2-bb44837c2d9d/GCF_020782115.1_ASM2078211v1_genomic.fna.gz --refList GCF_020782115.1_ASM2078211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020782115.1_ASM2078211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:59:54,628] [INFO] Task succeeded: fastANI
[2024-01-25 17:59:54,635] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:59:54,635] [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_002744755.1	s__Leeuwenhoekiella nanhaiensis	89.2971	1135	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCA_002708845.1	s__Leeuwenhoekiella sp002708845	82.9164	1015	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.1804	560	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	79.0743	495	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	78.8556	559	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	78.8162	498	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.5202	492	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	77.7628	443	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	76.6093	62	1442	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:59:54,636] [INFO] GTDB search result was written to GCF_020782115.1_ASM2078211v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:59:54,637] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:59:54,639] [INFO] DFAST_QC result json was written to GCF_020782115.1_ASM2078211v1_genomic.fna/dqc_result.json
[2024-01-25 17:59:54,640] [INFO] DFAST_QC completed!
[2024-01-25 17:59:54,640] [INFO] Total running time: 0h1m19s