[2023-06-28 19:48:10,849] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:10,861] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:10,862] [INFO] DQC Reference Directory: /var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference
[2023-06-28 19:48:12,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:12,574] [INFO] Task started: Prodigal
[2023-06-28 19:48:12,574] [INFO] Running command: gunzip -c /var/lib/cwl/stg230e8129-585e-4adc-8b38-88cda6550f58/GCA_002708845.1_ASM270884v1_genomic.fna.gz | prodigal -d GCA_002708845.1_ASM270884v1_genomic.fna/cds.fna -a GCA_002708845.1_ASM270884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:29,270] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:29,271] [INFO] Task started: HMMsearch
[2023-06-28 19:48:29,271] [INFO] Running command: hmmsearch --tblout GCA_002708845.1_ASM270884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference/reference_markers.hmm GCA_002708845.1_ASM270884v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:29,604] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:29,606] [INFO] Found 6/6 markers.
[2023-06-28 19:48:29,648] [INFO] Query marker FASTA was written to GCA_002708845.1_ASM270884v1_genomic.fna/markers.fasta
[2023-06-28 19:48:29,648] [INFO] Task started: Blastn
[2023-06-28 19:48:29,649] [INFO] Running command: blastn -query GCA_002708845.1_ASM270884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference/reference_markers.fasta -out GCA_002708845.1_ASM270884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:30,348] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:30,360] [INFO] Selected 18 target genomes.
[2023-06-28 19:48:30,360] [INFO] Target genome list was writen to GCA_002708845.1_ASM270884v1_genomic.fna/target_genomes.txt
[2023-06-28 19:48:30,411] [INFO] Task started: fastANI
[2023-06-28 19:48:30,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg230e8129-585e-4adc-8b38-88cda6550f58/GCA_002708845.1_ASM270884v1_genomic.fna.gz --refList GCA_002708845.1_ASM270884v1_genomic.fna/target_genomes.txt --output GCA_002708845.1_ASM270884v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:43,405] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:43,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:43,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:43,418] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:43,418] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:48:43,419] [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	84.0171	1046	1430	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	81.8729	610	1430	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	78.8235	528	1430	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	78.8083	534	1430	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	78.6061	473	1430	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	78.4811	469	1430	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.3267	468	1430	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	77.9185	280	1430	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	76.2881	60	1430	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	76.2881	60	1430	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.0994	67	1430	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	75.8013	72	1430	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	75.6937	56	1430	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.5419	63	1430	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:43,421] [INFO] DFAST Taxonomy check result was written to GCA_002708845.1_ASM270884v1_genomic.fna/tc_result.tsv
[2023-06-28 19:48:43,422] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:43,422] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:43,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference/checkm_data
[2023-06-28 19:48:43,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:43,466] [INFO] Task started: CheckM
[2023-06-28 19:48:43,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708845.1_ASM270884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708845.1_ASM270884v1_genomic.fna/checkm_input GCA_002708845.1_ASM270884v1_genomic.fna/checkm_result
[2023-06-28 19:49:33,128] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:33,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:33,152] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:33,153] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:33,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708845.1_ASM270884v1_genomic.fna/markers.fasta)
[2023-06-28 19:49:33,153] [INFO] Task started: Blastn
[2023-06-28 19:49:33,154] [INFO] Running command: blastn -query GCA_002708845.1_ASM270884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga3adce9f-e5fb-481a-a58c-9f37c8f1be8d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708845.1_ASM270884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:33,994] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:33,999] [INFO] Selected 11 target genomes.
[2023-06-28 19:49:34,000] [INFO] Target genome list was writen to GCA_002708845.1_ASM270884v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:34,006] [INFO] Task started: fastANI
[2023-06-28 19:49:34,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg230e8129-585e-4adc-8b38-88cda6550f58/GCA_002708845.1_ASM270884v1_genomic.fna.gz --refList GCA_002708845.1_ASM270884v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708845.1_ASM270884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:42,921] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:42,935] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:49:42,936] [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_002708845.1	s__Leeuwenhoekiella sp002708845	100.0	1427	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.96	99.95	0.93	0.90	5	conclusive
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	84.0171	1046	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	81.8694	610	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	81.5071	639	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	78.8209	533	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	78.588	475	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.3519	465	1430	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	77.939	420	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	77.9185	280	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	76.2881	60	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:42,938] [INFO] GTDB search result was written to GCA_002708845.1_ASM270884v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:42,938] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:42,942] [INFO] DFAST_QC result json was written to GCA_002708845.1_ASM270884v1_genomic.fna/dqc_result.json
[2023-06-28 19:49:42,943] [INFO] DFAST_QC completed!
[2023-06-28 19:49:42,943] [INFO] Total running time: 0h1m32s