[2023-06-29 23:15:46,734] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:15:46,738] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:15:46,738] [INFO] DQC Reference Directory: /var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference
[2023-06-29 23:15:48,072] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:15:48,075] [INFO] Task started: Prodigal
[2023-06-29 23:15:48,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ee05e8c-57a3-45ac-a903-6eddd8cbfaa3/GCA_016708305.1_ASM1670830v1_genomic.fna.gz | prodigal -d GCA_016708305.1_ASM1670830v1_genomic.fna/cds.fna -a GCA_016708305.1_ASM1670830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:16:06,632] [INFO] Task succeeded: Prodigal
[2023-06-29 23:16:06,632] [INFO] Task started: HMMsearch
[2023-06-29 23:16:06,632] [INFO] Running command: hmmsearch --tblout GCA_016708305.1_ASM1670830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference/reference_markers.hmm GCA_016708305.1_ASM1670830v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:16:06,941] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:16:06,942] [INFO] Found 6/6 markers.
[2023-06-29 23:16:06,980] [INFO] Query marker FASTA was written to GCA_016708305.1_ASM1670830v1_genomic.fna/markers.fasta
[2023-06-29 23:16:06,981] [INFO] Task started: Blastn
[2023-06-29 23:16:06,981] [INFO] Running command: blastn -query GCA_016708305.1_ASM1670830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference/reference_markers.fasta -out GCA_016708305.1_ASM1670830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:16:07,668] [INFO] Task succeeded: Blastn
[2023-06-29 23:16:07,673] [INFO] Selected 31 target genomes.
[2023-06-29 23:16:07,674] [INFO] Target genome list was writen to GCA_016708305.1_ASM1670830v1_genomic.fna/target_genomes.txt
[2023-06-29 23:16:07,676] [INFO] Task started: fastANI
[2023-06-29 23:16:07,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee05e8c-57a3-45ac-a903-6eddd8cbfaa3/GCA_016708305.1_ASM1670830v1_genomic.fna.gz --refList GCA_016708305.1_ASM1670830v1_genomic.fna/target_genomes.txt --output GCA_016708305.1_ASM1670830v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:16:34,436] [INFO] Task succeeded: fastANI
[2023-06-29 23:16:34,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:16:34,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:16:34,446] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:16:34,447] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:16:34,447] [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
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	76.5186	70	1356	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	76.4824	72	1356	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	76.155	69	1356	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.1118	50	1356	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.09	51	1356	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	76.0869	70	1356	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	75.9894	85	1356	95	below_threshold
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	75.8382	69	1356	95	below_threshold
Niabella yanshanensis	strain=HAMBI_3031	GCA_003349965.1	577386	577386	type	True	75.8283	80	1356	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	75.3228	52	1356	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:16:34,449] [INFO] DFAST Taxonomy check result was written to GCA_016708305.1_ASM1670830v1_genomic.fna/tc_result.tsv
[2023-06-29 23:16:34,449] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:16:34,449] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:16:34,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference/checkm_data
[2023-06-29 23:16:34,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:16:34,497] [INFO] Task started: CheckM
[2023-06-29 23:16:34,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708305.1_ASM1670830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708305.1_ASM1670830v1_genomic.fna/checkm_input GCA_016708305.1_ASM1670830v1_genomic.fna/checkm_result
[2023-06-29 23:17:29,114] [INFO] Task succeeded: CheckM
[2023-06-29 23:17:29,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:17:29,139] [INFO] ===== Completeness check finished =====
[2023-06-29 23:17:29,139] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:17:29,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708305.1_ASM1670830v1_genomic.fna/markers.fasta)
[2023-06-29 23:17:29,140] [INFO] Task started: Blastn
[2023-06-29 23:17:29,140] [INFO] Running command: blastn -query GCA_016708305.1_ASM1670830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17d0bb96-309d-4ac8-a2f0-117355d6af68/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708305.1_ASM1670830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:17:30,039] [INFO] Task succeeded: Blastn
[2023-06-29 23:17:30,044] [INFO] Selected 32 target genomes.
[2023-06-29 23:17:30,044] [INFO] Target genome list was writen to GCA_016708305.1_ASM1670830v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:17:30,087] [INFO] Task started: fastANI
[2023-06-29 23:17:30,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee05e8c-57a3-45ac-a903-6eddd8cbfaa3/GCA_016708305.1_ASM1670830v1_genomic.fna.gz --refList GCA_016708305.1_ASM1670830v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708305.1_ASM1670830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:17:54,324] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:54,342] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:17:54,343] [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_016708305.1	s__Niabella sp016708305	100.0	1355	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001654455.1	s__Niabella ginsenosidivorans	76.5186	70	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374125.1	s__Niabella aurantiaca	76.4824	72	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243115.2	s__Niabella soli	76.3929	70	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399735.1	s__Terrimonas sp002399735	76.2391	52	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Terrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233845.1	s__Ilyomonas limi	76.1118	50	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ilyomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744715.1	s__Niabella sp017744715	76.0	84	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349965.1	s__Niabella yanshanensis	75.813	81	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268055.1	s__JJ008 sp018268055	75.6807	52	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898485.1	s__46-32 sp001898485	75.6541	57	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCA_005882315.1	s__VBAR01 sp005882315	75.6528	53	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744795.1	s__Niabella sp017744795	75.6413	52	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115755.1	s__Parafilimonas terrae	75.3355	51	1356	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 23:17:54,345] [INFO] GTDB search result was written to GCA_016708305.1_ASM1670830v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:17:54,345] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:17:54,349] [INFO] DFAST_QC result json was written to GCA_016708305.1_ASM1670830v1_genomic.fna/dqc_result.json
[2023-06-29 23:17:54,349] [INFO] DFAST_QC completed!
[2023-06-29 23:17:54,349] [INFO] Total running time: 0h2m8s