[2024-01-24 10:47:06,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,103] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a975b76-31a3-4146-86d8-67c936ad0d4c/GCF_024437655.1_ASM2443765v1_genomic.fna.gz | prodigal -d GCF_024437655.1_ASM2443765v1_genomic.fna/cds.fna -a GCF_024437655.1_ASM2443765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,686] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,686] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,686] [INFO] Running command: hmmsearch --tblout GCF_024437655.1_ASM2443765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference/reference_markers.hmm GCF_024437655.1_ASM2443765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,974] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,976] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,009] [INFO] Query marker FASTA was written to GCF_024437655.1_ASM2443765v1_genomic.fna/markers.fasta
[2024-01-24 10:47:25,010] [INFO] Task started: Blastn
[2024-01-24 10:47:25,010] [INFO] Running command: blastn -query GCF_024437655.1_ASM2443765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference/reference_markers.fasta -out GCF_024437655.1_ASM2443765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,940] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,944] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:25,944] [INFO] Target genome list was writen to GCF_024437655.1_ASM2443765v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:25,968] [INFO] Task started: fastANI
[2024-01-24 10:47:25,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a975b76-31a3-4146-86d8-67c936ad0d4c/GCF_024437655.1_ASM2443765v1_genomic.fna.gz --refList GCF_024437655.1_ASM2443765v1_genomic.fna/target_genomes.txt --output GCF_024437655.1_ASM2443765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:42,433] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:42,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:42,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:42,449] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:42,450] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:42,450] [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	81.7043	771	1273	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	80.8272	691	1273	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	79.8351	523	1273	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	79.6679	544	1273	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	79.3905	549	1273	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	78.9434	449	1273	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.7824	455	1273	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.4626	374	1273	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	78.1729	316	1273	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	78.1179	275	1273	95	below_threshold
Silvimonas iriomotensis	strain=CGMCC 1.8859	GCA_014645535.1	449662	449662	type	True	78.0435	349	1273	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	77.6999	267	1273	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	77.6757	285	1273	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.7466	161	1273	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.6954	228	1273	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	76.483	185	1273	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	76.263	223	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:42,459] [INFO] DFAST Taxonomy check result was written to GCF_024437655.1_ASM2443765v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:42,460] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:42,461] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:42,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference/checkm_data
[2024-01-24 10:47:42,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:42,502] [INFO] Task started: CheckM
[2024-01-24 10:47:42,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024437655.1_ASM2443765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024437655.1_ASM2443765v1_genomic.fna/checkm_input GCF_024437655.1_ASM2443765v1_genomic.fna/checkm_result
[2024-01-24 10:48:20,732] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:20,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,754] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:20,754] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:20,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024437655.1_ASM2443765v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:20,755] [INFO] Task started: Blastn
[2024-01-24 10:48:20,755] [INFO] Running command: blastn -query GCF_024437655.1_ASM2443765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f8507a7-d5d2-4abb-a2b2-ab73dff3a687/dqc_reference/reference_markers_gtdb.fasta -out GCF_024437655.1_ASM2443765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:22,357] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:22,361] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:22,361] [INFO] Target genome list was writen to GCF_024437655.1_ASM2443765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:22,370] [INFO] Task started: fastANI
[2024-01-24 10:48:22,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a975b76-31a3-4146-86d8-67c936ad0d4c/GCF_024437655.1_ASM2443765v1_genomic.fna.gz --refList GCF_024437655.1_ASM2443765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024437655.1_ASM2443765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:32,615] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:32,627] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:32,627] [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	85.9128	990	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	81.7209	768	1273	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	80.8252	690	1273	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	80.0724	548	1273	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	79.6929	541	1273	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	79.3765	551	1273	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	79.352	529	1273	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	79.1691	487	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	78.9623	448	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430805.1	s__Chitinilyticum aquatile	78.4826	372	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115065.1	s__Formivibrio citricus	78.1309	274	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261735.1	s__Formivibrio sp018261735	77.9353	282	1273	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	77.6757	285	1273	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 10:48:32,629] [INFO] GTDB search result was written to GCF_024437655.1_ASM2443765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:32,629] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:32,633] [INFO] DFAST_QC result json was written to GCF_024437655.1_ASM2443765v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:32,634] [INFO] DFAST_QC completed!
[2024-01-24 10:48:32,634] [INFO] Total running time: 0h1m26s