[2024-01-24 14:05:36,481] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,483] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,483] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference
[2024-01-24 14:05:37,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,792] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgac60a8de-866a-4bb8-9121-2b18a71a33ce/GCF_014652315.1_ASM1465231v1_genomic.fna.gz | prodigal -d GCF_014652315.1_ASM1465231v1_genomic.fna/cds.fna -a GCF_014652315.1_ASM1465231v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:50,447] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:50,447] [INFO] Task started: HMMsearch
[2024-01-24 14:05:50,447] [INFO] Running command: hmmsearch --tblout GCF_014652315.1_ASM1465231v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference/reference_markers.hmm GCF_014652315.1_ASM1465231v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:50,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:50,768] [INFO] Found 6/6 markers.
[2024-01-24 14:05:50,823] [INFO] Query marker FASTA was written to GCF_014652315.1_ASM1465231v1_genomic.fna/markers.fasta
[2024-01-24 14:05:50,823] [INFO] Task started: Blastn
[2024-01-24 14:05:50,823] [INFO] Running command: blastn -query GCF_014652315.1_ASM1465231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference/reference_markers.fasta -out GCF_014652315.1_ASM1465231v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:51,732] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:51,735] [INFO] Selected 14 target genomes.
[2024-01-24 14:05:51,736] [INFO] Target genome list was writen to GCF_014652315.1_ASM1465231v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:51,744] [INFO] Task started: fastANI
[2024-01-24 14:05:51,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgac60a8de-866a-4bb8-9121-2b18a71a33ce/GCF_014652315.1_ASM1465231v1_genomic.fna.gz --refList GCF_014652315.1_ASM1465231v1_genomic.fna/target_genomes.txt --output GCF_014652315.1_ASM1465231v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:06,260] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:06,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:06,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:06,275] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:06,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:06,275] [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
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	100.0	1291	1293	95	conclusive
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	89.847	1105	1293	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	80.0799	628	1293	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	79.8173	515	1293	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	79.5614	499	1293	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	79.2577	477	1293	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	79.1281	456	1293	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	78.5946	501	1293	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.5259	398	1293	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	77.9781	279	1293	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	77.1953	149	1293	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.1921	260	1293	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	77.0509	209	1293	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	76.9579	233	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,277] [INFO] DFAST Taxonomy check result was written to GCF_014652315.1_ASM1465231v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:06,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:06,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:06,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference/checkm_data
[2024-01-24 14:06:06,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:06,324] [INFO] Task started: CheckM
[2024-01-24 14:06:06,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652315.1_ASM1465231v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652315.1_ASM1465231v1_genomic.fna/checkm_input GCF_014652315.1_ASM1465231v1_genomic.fna/checkm_result
[2024-01-24 14:06:48,237] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:48,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:48,260] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:48,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:48,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652315.1_ASM1465231v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:48,261] [INFO] Task started: Blastn
[2024-01-24 14:06:48,261] [INFO] Running command: blastn -query GCF_014652315.1_ASM1465231v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ca8529f-a30d-4781-aa35-fa877aa05b90/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652315.1_ASM1465231v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:50,044] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:50,048] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:50,048] [INFO] Target genome list was writen to GCF_014652315.1_ASM1465231v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:50,056] [INFO] Task started: fastANI
[2024-01-24 14:06:50,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgac60a8de-866a-4bb8-9121-2b18a71a33ce/GCF_014652315.1_ASM1465231v1_genomic.fna.gz --refList GCF_014652315.1_ASM1465231v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652315.1_ASM1465231v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:59,603] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:59,618] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:59,619] [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_014652315.1	s__Jeongeupia chitinilytica	100.0	1291	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016865585.1	s__Jeongeupia naejangsanensis	89.8495	1104	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001808185.1	s__Jeongeupia sp001808185	88.0092	1010	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015140455.1	s__Jeongeupia sp015140455	84.6056	909	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	80.1443	620	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	79.7658	520	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	79.7343	548	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	79.2679	476	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	79.1089	458	1293	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	78.5259	398	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,621] [INFO] GTDB search result was written to GCF_014652315.1_ASM1465231v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:59,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:59,625] [INFO] DFAST_QC result json was written to GCF_014652315.1_ASM1465231v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:59,625] [INFO] DFAST_QC completed!
[2024-01-24 14:06:59,625] [INFO] Total running time: 0h1m23s