[2024-01-24 15:26:32,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:32,954] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:32,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference
[2024-01-24 15:26:34,194] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:34,195] [INFO] Task started: Prodigal
[2024-01-24 15:26:34,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg671e4034-2dd7-4b28-b020-2998632007cd/GCF_004834005.1_ASM483400v1_genomic.fna.gz | prodigal -d GCF_004834005.1_ASM483400v1_genomic.fna/cds.fna -a GCF_004834005.1_ASM483400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:12,748] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:12,749] [INFO] Task started: HMMsearch
[2024-01-24 15:27:12,749] [INFO] Running command: hmmsearch --tblout GCF_004834005.1_ASM483400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference/reference_markers.hmm GCF_004834005.1_ASM483400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:13,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:13,161] [INFO] Found 6/6 markers.
[2024-01-24 15:27:13,223] [INFO] Query marker FASTA was written to GCF_004834005.1_ASM483400v1_genomic.fna/markers.fasta
[2024-01-24 15:27:13,224] [INFO] Task started: Blastn
[2024-01-24 15:27:13,224] [INFO] Running command: blastn -query GCF_004834005.1_ASM483400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference/reference_markers.fasta -out GCF_004834005.1_ASM483400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:13,843] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:14,041] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:14,042] [INFO] Target genome list was writen to GCF_004834005.1_ASM483400v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:14,051] [INFO] Task started: fastANI
[2024-01-24 15:27:14,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg671e4034-2dd7-4b28-b020-2998632007cd/GCF_004834005.1_ASM483400v1_genomic.fna.gz --refList GCF_004834005.1_ASM483400v1_genomic.fna/target_genomes.txt --output GCF_004834005.1_ASM483400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:35,224] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:35,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:35,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:35,248] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:35,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:35,249] [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
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	100.0	2689	2691	95	conclusive
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	82.157	1671	2691	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	81.119	1414	2691	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	80.7852	1254	2691	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	80.7402	1259	2691	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	80.717	1282	2691	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	80.6041	1353	2691	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	80.4991	1362	2691	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.094	93	2691	95	below_threshold
Flavihumibacter petaseus	strain=NBRC 106054	GCA_000974785.1	549295	549295	type	True	76.0329	89	2691	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0164	103	2691	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	75.9091	86	2691	95	below_threshold
Niabella hibiscisoli	strain=THG-DN5.5	GCA_022512515.1	1825928	1825928	type	True	75.7801	75	2691	95	below_threshold
Chitinophaga hostae	strain=2R12	GCA_018224885.1	2831022	2831022	type	True	75.5398	82	2691	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	75.5111	58	2691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:35,251] [INFO] DFAST Taxonomy check result was written to GCF_004834005.1_ASM483400v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:35,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:35,253] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:35,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference/checkm_data
[2024-01-24 15:27:35,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:35,331] [INFO] Task started: CheckM
[2024-01-24 15:27:35,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004834005.1_ASM483400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004834005.1_ASM483400v1_genomic.fna/checkm_input GCF_004834005.1_ASM483400v1_genomic.fna/checkm_result
[2024-01-24 15:29:17,711] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:17,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:17,740] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:17,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:17,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004834005.1_ASM483400v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:17,742] [INFO] Task started: Blastn
[2024-01-24 15:29:17,742] [INFO] Running command: blastn -query GCF_004834005.1_ASM483400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb46b6fef-b9ef-4fb0-a744-cc71209244b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004834005.1_ASM483400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:18,540] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:18,545] [INFO] Selected 11 target genomes.
[2024-01-24 15:29:18,546] [INFO] Target genome list was writen to GCF_004834005.1_ASM483400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:18,556] [INFO] Task started: fastANI
[2024-01-24 15:29:18,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg671e4034-2dd7-4b28-b020-2998632007cd/GCF_004834005.1_ASM483400v1_genomic.fna.gz --refList GCF_004834005.1_ASM483400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004834005.1_ASM483400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:37,713] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:37,775] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:37,776] [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_004834005.1	s__Niastella caeni	100.0	2689	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002077945.1	s__Niastella vici	82.157	1671	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356035.1	s__Niastella sp017356035	81.2158	1347	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341975.1	s__Niastella sp004341975	81.1612	1478	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078015.1	s__Niastella populi	81.1115	1416	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924755.1	s__Niastella sp016924755	81.0387	1354	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	80.7903	1253	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017742245.1	s__Niastella sp017742245	80.7201	1282	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	80.6037	1352	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017849455.1	s__Pseudobacter sp017849455	76.6915	261	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971225.1	s__Panacibacter ginsenosidivorans	75.9091	86	2691	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:37,777] [INFO] GTDB search result was written to GCF_004834005.1_ASM483400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:37,780] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:37,784] [INFO] DFAST_QC result json was written to GCF_004834005.1_ASM483400v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:37,785] [INFO] DFAST_QC completed!
[2024-01-24 15:29:37,785] [INFO] Total running time: 0h3m5s