[2024-01-25 20:00:50,531] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:50,535] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:50,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference
[2024-01-25 20:00:51,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:51,716] [INFO] Task started: Prodigal
[2024-01-25 20:00:51,717] [INFO] Running command: gunzip -c /var/lib/cwl/stg7633a5d3-5f80-4da9-8e44-b869d0dfa7d7/GCF_016865585.1_ASM1686558v1_genomic.fna.gz | prodigal -d GCF_016865585.1_ASM1686558v1_genomic.fna/cds.fna -a GCF_016865585.1_ASM1686558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:02,322] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:02,322] [INFO] Task started: HMMsearch
[2024-01-25 20:01:02,322] [INFO] Running command: hmmsearch --tblout GCF_016865585.1_ASM1686558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference/reference_markers.hmm GCF_016865585.1_ASM1686558v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:02,560] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:02,561] [INFO] Found 6/6 markers.
[2024-01-25 20:01:02,594] [INFO] Query marker FASTA was written to GCF_016865585.1_ASM1686558v1_genomic.fna/markers.fasta
[2024-01-25 20:01:02,594] [INFO] Task started: Blastn
[2024-01-25 20:01:02,594] [INFO] Running command: blastn -query GCF_016865585.1_ASM1686558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference/reference_markers.fasta -out GCF_016865585.1_ASM1686558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:03,454] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:03,461] [INFO] Selected 14 target genomes.
[2024-01-25 20:01:03,462] [INFO] Target genome list was writen to GCF_016865585.1_ASM1686558v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:03,473] [INFO] Task started: fastANI
[2024-01-25 20:01:03,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg7633a5d3-5f80-4da9-8e44-b869d0dfa7d7/GCF_016865585.1_ASM1686558v1_genomic.fna.gz --refList GCF_016865585.1_ASM1686558v1_genomic.fna/target_genomes.txt --output GCF_016865585.1_ASM1686558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:15,830] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:15,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:15,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:15,840] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:15,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:15,841] [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 naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	100.0	1293	1294	95	conclusive
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	89.8842	1103	1294	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	80.1084	594	1294	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	79.7845	513	1294	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	79.0697	486	1294	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	79.061	453	1294	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	79.0438	524	1294	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	78.6724	360	1294	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	78.5908	400	1294	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	78.5627	461	1294	95	below_threshold
Cupriavidus cauae	strain=MKL-01	GCA_008632125.1	2608999	2608999	type	True	77.479	277	1294	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	77.2596	246	1294	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	77.1748	158	1294	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	76.8247	180	1294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:15,842] [INFO] DFAST Taxonomy check result was written to GCF_016865585.1_ASM1686558v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:15,842] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:15,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:15,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference/checkm_data
[2024-01-25 20:01:15,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:15,882] [INFO] Task started: CheckM
[2024-01-25 20:01:15,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016865585.1_ASM1686558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016865585.1_ASM1686558v1_genomic.fna/checkm_input GCF_016865585.1_ASM1686558v1_genomic.fna/checkm_result
[2024-01-25 20:01:50,590] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:50,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:50,631] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:50,631] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:50,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016865585.1_ASM1686558v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:50,632] [INFO] Task started: Blastn
[2024-01-25 20:01:50,632] [INFO] Running command: blastn -query GCF_016865585.1_ASM1686558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg715f3519-c1ef-41e7-84f3-a2000afccf2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016865585.1_ASM1686558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:52,318] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:52,321] [INFO] Selected 9 target genomes.
[2024-01-25 20:01:52,321] [INFO] Target genome list was writen to GCF_016865585.1_ASM1686558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:52,331] [INFO] Task started: fastANI
[2024-01-25 20:01:52,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg7633a5d3-5f80-4da9-8e44-b869d0dfa7d7/GCF_016865585.1_ASM1686558v1_genomic.fna.gz --refList GCF_016865585.1_ASM1686558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016865585.1_ASM1686558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:00,532] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:00,539] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:00,539] [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_016865585.1	s__Jeongeupia naejangsanensis	100.0	1293	1294	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_014652315.1	s__Jeongeupia chitinilytica	89.8914	1102	1294	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	87.6939	1001	1294	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	84.5262	920	1294	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	80.1275	592	1294	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	79.8004	511	1294	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	79.7427	542	1294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848685.1	s__Andreprevotia sp009848685	79.1829	497	1294	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	79.0817	451	1294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:00,540] [INFO] GTDB search result was written to GCF_016865585.1_ASM1686558v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:00,541] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:00,544] [INFO] DFAST_QC result json was written to GCF_016865585.1_ASM1686558v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:00,544] [INFO] DFAST_QC completed!
[2024-01-25 20:02:00,544] [INFO] Total running time: 0h1m10s