[2024-01-24 13:01:12,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference
[2024-01-24 13:01:14,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:14,061] [INFO] Task started: Prodigal
[2024-01-24 13:01:14,061] [INFO] Running command: gunzip -c /var/lib/cwl/stg41d428c5-844d-48fc-b959-986f83de8ceb/GCF_000430805.1_ASM43080v1_genomic.fna.gz | prodigal -d GCF_000430805.1_ASM43080v1_genomic.fna/cds.fna -a GCF_000430805.1_ASM43080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:26,043] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:26,043] [INFO] Task started: HMMsearch
[2024-01-24 13:01:26,044] [INFO] Running command: hmmsearch --tblout GCF_000430805.1_ASM43080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference/reference_markers.hmm GCF_000430805.1_ASM43080v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:26,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:26,332] [INFO] Found 6/6 markers.
[2024-01-24 13:01:26,380] [INFO] Query marker FASTA was written to GCF_000430805.1_ASM43080v1_genomic.fna/markers.fasta
[2024-01-24 13:01:26,380] [INFO] Task started: Blastn
[2024-01-24 13:01:26,380] [INFO] Running command: blastn -query GCF_000430805.1_ASM43080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference/reference_markers.fasta -out GCF_000430805.1_ASM43080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:27,243] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:27,253] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:27,254] [INFO] Target genome list was writen to GCF_000430805.1_ASM43080v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:27,260] [INFO] Task started: fastANI
[2024-01-24 13:01:27,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d428c5-844d-48fc-b959-986f83de8ceb/GCF_000430805.1_ASM43080v1_genomic.fna.gz --refList GCF_000430805.1_ASM43080v1_genomic.fna/target_genomes.txt --output GCF_000430805.1_ASM43080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:38,911] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:38,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:38,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:38,925] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:38,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:38,925] [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
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	100.0	1216	1216	95	conclusive
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	84.7334	799	1216	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	84.4345	817	1216	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	78.8055	406	1216	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	78.7284	390	1216	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	78.5408	417	1216	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	78.4917	393	1216	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	78.2187	374	1216	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	78.1785	352	1216	95	below_threshold
Formivibrio citricus	strain=DSM 6150	GCA_900115065.1	83765	83765	type	True	78.0797	253	1216	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	76.2874	91	1216	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	76.1067	117	1216	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	76.0007	93	1216	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	75.779	92	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:38,930] [INFO] DFAST Taxonomy check result was written to GCF_000430805.1_ASM43080v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:38,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:38,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:38,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference/checkm_data
[2024-01-24 13:01:38,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:38,970] [INFO] Task started: CheckM
[2024-01-24 13:01:38,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430805.1_ASM43080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430805.1_ASM43080v1_genomic.fna/checkm_input GCF_000430805.1_ASM43080v1_genomic.fna/checkm_result
[2024-01-24 13:02:16,298] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:16,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:16,322] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:16,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:16,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430805.1_ASM43080v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:16,323] [INFO] Task started: Blastn
[2024-01-24 13:02:16,324] [INFO] Running command: blastn -query GCF_000430805.1_ASM43080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a8e78be-3e3a-421e-9dd7-1761a11a3d56/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430805.1_ASM43080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:17,835] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:17,839] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:17,839] [INFO] Target genome list was writen to GCF_000430805.1_ASM43080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:17,850] [INFO] Task started: fastANI
[2024-01-24 13:02:17,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d428c5-844d-48fc-b959-986f83de8ceb/GCF_000430805.1_ASM43080v1_genomic.fna.gz --refList GCF_000430805.1_ASM43080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430805.1_ASM43080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:28,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:28,139] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:28,139] [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_000430805.1	s__Chitinilyticum aquatile	100.0	1216	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015223195.1	s__Chitinilyticum litopenaei_A	84.7368	798	1216	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	84.4193	819	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	78.8008	407	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865585.1	s__Jeongeupia naejangsanensis	78.7287	390	1216	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	78.6998	399	1216	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	78.5225	420	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	78.5023	392	1216	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	78.4443	379	1216	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	78.3334	399	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015140455.1	s__Jeongeupia sp015140455	78.187	375	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711875.1	s__Andreprevotia chitinilytica	78.1796	352	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261735.1	s__Formivibrio sp018261735	78.0776	269	1216	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Formivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115065.1	s__Formivibrio citricus	78.0657	254	1216	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 13:02:28,141] [INFO] GTDB search result was written to GCF_000430805.1_ASM43080v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:28,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:28,146] [INFO] DFAST_QC result json was written to GCF_000430805.1_ASM43080v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:28,146] [INFO] DFAST_QC completed!
[2024-01-24 13:02:28,147] [INFO] Total running time: 0h1m16s