[2024-01-25 19:40:35,515] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:35,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:35,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference
[2024-01-25 19:40:36,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:36,713] [INFO] Task started: Prodigal
[2024-01-25 19:40:36,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c67dfbb-2555-4fd6-970e-2c763cadb524/GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/cds.fna -a GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:45,343] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:45,344] [INFO] Task started: HMMsearch
[2024-01-25 19:40:45,344] [INFO] Running command: hmmsearch --tblout GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference/reference_markers.hmm GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:45,568] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:45,569] [INFO] Found 6/6 markers.
[2024-01-25 19:40:45,593] [INFO] Query marker FASTA was written to GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:40:45,593] [INFO] Task started: Blastn
[2024-01-25 19:40:45,593] [INFO] Running command: blastn -query GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference/reference_markers.fasta -out GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:46,395] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:46,398] [INFO] Selected 18 target genomes.
[2024-01-25 19:40:46,398] [INFO] Target genome list was writen to GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:40:46,405] [INFO] Task started: fastANI
[2024-01-25 19:40:46,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c67dfbb-2555-4fd6-970e-2c763cadb524/GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna.gz --refList GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:41:02,113] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:02,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:41:02,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:41:02,125] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:41:02,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:41:02,125] [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
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	100.0	1000	1001	95	conclusive
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	78.4173	309	1001	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	78.3688	272	1001	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	78.3562	266	1001	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	78.2736	279	1001	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	78.1006	300	1001	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.0759	249	1001	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	77.9836	246	1001	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.9247	300	1001	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	77.9213	266	1001	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	77.6189	173	1001	95	below_threshold
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	77.326	157	1001	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	77.3111	182	1001	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	77.2086	181	1001	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	76.7527	133	1001	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	76.5997	152	1001	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	76.5556	103	1001	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	76.2155	110	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:41:02,127] [INFO] DFAST Taxonomy check result was written to GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:41:02,127] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:41:02,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:41:02,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference/checkm_data
[2024-01-25 19:41:02,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:41:02,159] [INFO] Task started: CheckM
[2024-01-25 19:41:02,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/checkm_input GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:41:30,113] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:30,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:30,132] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:30,132] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:30,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:41:30,133] [INFO] Task started: Blastn
[2024-01-25 19:41:30,133] [INFO] Running command: blastn -query GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg404a3874-e6b6-4df2-897d-603ae06a53c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:31,671] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:31,674] [INFO] Selected 13 target genomes.
[2024-01-25 19:41:31,675] [INFO] Target genome list was writen to GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:31,688] [INFO] Task started: fastANI
[2024-01-25 19:41:31,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c67dfbb-2555-4fd6-970e-2c763cadb524/GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna.gz --refList GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:41,837] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:41,846] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:41:41,846] [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_900115065.1	s__Formivibrio citricus	100.0	1000	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018261735.1	s__Formivibrio sp018261735	79.8706	441	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	78.406	310	1001	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	78.3931	299	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430805.1	s__Chitinilyticum aquatile	78.0906	248	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	78.088	301	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	78.0826	286	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	77.9235	300	1001	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	77.9212	266	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015140455.1	s__Jeongeupia sp015140455	77.9067	272	1001	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	77.7238	264	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645555.1	s__Silvimonas amylolytica	77.3428	156	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202765.1	s__Silvimonas terrae	77.3118	181	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:41,847] [INFO] GTDB search result was written to GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:41,848] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:41,851] [INFO] DFAST_QC result json was written to GCF_900115065.1_IMG-taxon_2599185172_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:41:41,851] [INFO] DFAST_QC completed!
[2024-01-25 19:41:41,851] [INFO] Total running time: 0h1m6s