[2024-01-24 13:21:40,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:40,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:40,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference
[2024-01-24 13:21:42,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:42,164] [INFO] Task started: Prodigal
[2024-01-24 13:21:42,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cc487d1-c226-402f-9695-c026475d2fe3/GCF_008033135.1_ASM803313v1_genomic.fna.gz | prodigal -d GCF_008033135.1_ASM803313v1_genomic.fna/cds.fna -a GCF_008033135.1_ASM803313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:04,568] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:04,568] [INFO] Task started: HMMsearch
[2024-01-24 13:22:04,569] [INFO] Running command: hmmsearch --tblout GCF_008033135.1_ASM803313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference/reference_markers.hmm GCF_008033135.1_ASM803313v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:04,846] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:04,847] [INFO] Found 6/6 markers.
[2024-01-24 13:22:04,899] [INFO] Query marker FASTA was written to GCF_008033135.1_ASM803313v1_genomic.fna/markers.fasta
[2024-01-24 13:22:04,900] [INFO] Task started: Blastn
[2024-01-24 13:22:04,900] [INFO] Running command: blastn -query GCF_008033135.1_ASM803313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference/reference_markers.fasta -out GCF_008033135.1_ASM803313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:05,772] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:05,777] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:05,778] [INFO] Target genome list was writen to GCF_008033135.1_ASM803313v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:05,793] [INFO] Task started: fastANI
[2024-01-24 13:22:05,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc487d1-c226-402f-9695-c026475d2fe3/GCF_008033135.1_ASM803313v1_genomic.fna.gz --refList GCF_008033135.1_ASM803313v1_genomic.fna/target_genomes.txt --output GCF_008033135.1_ASM803313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:20,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:20,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:20,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:20,492] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:20,492] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:20,492] [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
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	82.0346	829	1441	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	80.6981	748	1441	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	79.7239	555	1441	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	79.6914	537	1441	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	79.6346	560	1441	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	78.8714	462	1441	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.8529	485	1441	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.421	344	1441	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.3285	406	1441	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	78.2781	353	1441	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	78.262	278	1441	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.2171	280	1441	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	77.9174	296	1441	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.925	253	1441	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	76.8032	239	1441	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.5447	263	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:20,494] [INFO] DFAST Taxonomy check result was written to GCF_008033135.1_ASM803313v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:20,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:20,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:20,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference/checkm_data
[2024-01-24 13:22:20,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:20,540] [INFO] Task started: CheckM
[2024-01-24 13:22:20,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008033135.1_ASM803313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008033135.1_ASM803313v1_genomic.fna/checkm_input GCF_008033135.1_ASM803313v1_genomic.fna/checkm_result
[2024-01-24 13:23:29,097] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:29,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:29,114] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:29,115] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:29,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008033135.1_ASM803313v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:29,115] [INFO] Task started: Blastn
[2024-01-24 13:23:29,115] [INFO] Running command: blastn -query GCF_008033135.1_ASM803313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb116cbbc-8292-4f5e-a9ee-49930ddfebd0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008033135.1_ASM803313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:30,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:30,627] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:30,627] [INFO] Target genome list was writen to GCF_008033135.1_ASM803313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:30,634] [INFO] Task started: fastANI
[2024-01-24 13:23:30,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cc487d1-c226-402f-9695-c026475d2fe3/GCF_008033135.1_ASM803313v1_genomic.fna.gz --refList GCF_008033135.1_ASM803313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008033135.1_ASM803313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:39,797] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:39,807] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:39,807] [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_008033135.1	s__Chitinolyticbacter meiyuanensis	100.0	1438	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000374805.1	s__Chitiniphilus shinanonensis	82.0177	832	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048205.1	s__Chitiniphilus eburneus	80.669	750	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808185.1	s__Jeongeupia sp001808185	80.3004	559	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	79.7087	556	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	79.6831	538	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865585.1	s__Jeongeupia naejangsanensis	79.6254	561	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	79.4261	573	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	78.8792	482	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115065.1	s__Formivibrio citricus	78.2927	276	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001855565.1	s__Chromobacterium amazonense	78.2426	278	1441	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,808] [INFO] GTDB search result was written to GCF_008033135.1_ASM803313v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:39,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:39,812] [INFO] DFAST_QC result json was written to GCF_008033135.1_ASM803313v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:39,812] [INFO] DFAST_QC completed!
[2024-01-24 13:23:39,812] [INFO] Total running time: 0h1m59s