[2024-01-24 13:57:42,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference
[2024-01-24 13:57:43,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,662] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg82b8e44b-c3d8-4368-89a0-19e38e681b7b/GCF_030160775.1_ASM3016077v1_genomic.fna.gz | prodigal -d GCF_030160775.1_ASM3016077v1_genomic.fna/cds.fna -a GCF_030160775.1_ASM3016077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,966] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,966] [INFO] Running command: hmmsearch --tblout GCF_030160775.1_ASM3016077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference/reference_markers.hmm GCF_030160775.1_ASM3016077v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,323] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,325] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,365] [INFO] Query marker FASTA was written to GCF_030160775.1_ASM3016077v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,366] [INFO] Task started: Blastn
[2024-01-24 13:57:56,366] [INFO] Running command: blastn -query GCF_030160775.1_ASM3016077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference/reference_markers.fasta -out GCF_030160775.1_ASM3016077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,380] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,383] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:57,384] [INFO] Target genome list was writen to GCF_030160775.1_ASM3016077v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,390] [INFO] Task started: fastANI
[2024-01-24 13:57:57,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b8e44b-c3d8-4368-89a0-19e38e681b7b/GCF_030160775.1_ASM3016077v1_genomic.fna.gz --refList GCF_030160775.1_ASM3016077v1_genomic.fna/target_genomes.txt --output GCF_030160775.1_ASM3016077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:11,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:11,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:11,491] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:11,491] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:11,491] [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	99.9758	1259	1271	95	conclusive
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	87.0555	1084	1271	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	80.2047	586	1271	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	80.1598	564	1271	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	79.8204	579	1271	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	79.3884	582	1271	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	79.1763	479	1271	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	79.1187	490	1271	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.9622	392	1271	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.5686	393	1271	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	78.3404	300	1271	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.2939	378	1271	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.7788	322	1271	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.7008	329	1271	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7031	394	1271	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:11,493] [INFO] DFAST Taxonomy check result was written to GCF_030160775.1_ASM3016077v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:11,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:11,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:11,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference/checkm_data
[2024-01-24 13:58:11,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:11,537] [INFO] Task started: CheckM
[2024-01-24 13:58:11,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160775.1_ASM3016077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160775.1_ASM3016077v1_genomic.fna/checkm_input GCF_030160775.1_ASM3016077v1_genomic.fna/checkm_result
[2024-01-24 13:58:53,079] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:53,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,112] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:53,113] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:53,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160775.1_ASM3016077v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:53,113] [INFO] Task started: Blastn
[2024-01-24 13:58:53,114] [INFO] Running command: blastn -query GCF_030160775.1_ASM3016077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg488cb481-2037-41de-b59d-a618c664327a/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160775.1_ASM3016077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:54,989] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:54,992] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:54,992] [INFO] Target genome list was writen to GCF_030160775.1_ASM3016077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:55,022] [INFO] Task started: fastANI
[2024-01-24 13:58:55,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg82b8e44b-c3d8-4368-89a0-19e38e681b7b/GCF_030160775.1_ASM3016077v1_genomic.fna.gz --refList GCF_030160775.1_ASM3016077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160775.1_ASM3016077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:08,270] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:08,290] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:08,290] [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_000374805.1	s__Chitiniphilus shinanonensis	99.9758	1259	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005048205.1	s__Chitiniphilus eburneus	87.0672	1083	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	82.1582	776	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808185.1	s__Jeongeupia sp001808185	80.7806	613	1271	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	80.1825	589	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865585.1	s__Jeongeupia naejangsanensis	80.1599	564	1271	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	79.8484	576	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	79.5826	571	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428465.1	s__Chitinimonas koreensis	79.4055	583	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	79.1569	481	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	79.1187	490	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	78.9358	396	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCF_000430805.1	s__Chitinilyticum aquatile	78.5608	395	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261735.1	s__Formivibrio sp018261735	78.1607	311	1271	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:08,292] [INFO] GTDB search result was written to GCF_030160775.1_ASM3016077v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:08,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:08,296] [INFO] DFAST_QC result json was written to GCF_030160775.1_ASM3016077v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:08,296] [INFO] DFAST_QC completed!
[2024-01-24 13:59:08,297] [INFO] Total running time: 0h1m26s