[2024-01-25 17:34:07,123] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,126] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference
[2024-01-25 17:34:09,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,026] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,027] [INFO] Running command: gunzip -c /var/lib/cwl/stgca6a3e68-3372-4761-a64c-d2018dc930e3/GCF_016881405.1_ASM1688140v1_genomic.fna.gz | prodigal -d GCF_016881405.1_ASM1688140v1_genomic.fna/cds.fna -a GCF_016881405.1_ASM1688140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:17,537] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:17,538] [INFO] Task started: HMMsearch
[2024-01-25 17:34:17,538] [INFO] Running command: hmmsearch --tblout GCF_016881405.1_ASM1688140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference/reference_markers.hmm GCF_016881405.1_ASM1688140v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:17,814] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:17,815] [INFO] Found 6/6 markers.
[2024-01-25 17:34:17,846] [INFO] Query marker FASTA was written to GCF_016881405.1_ASM1688140v1_genomic.fna/markers.fasta
[2024-01-25 17:34:17,846] [INFO] Task started: Blastn
[2024-01-25 17:34:17,847] [INFO] Running command: blastn -query GCF_016881405.1_ASM1688140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference/reference_markers.fasta -out GCF_016881405.1_ASM1688140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:18,487] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:18,489] [INFO] Selected 15 target genomes.
[2024-01-25 17:34:18,490] [INFO] Target genome list was writen to GCF_016881405.1_ASM1688140v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:18,494] [INFO] Task started: fastANI
[2024-01-25 17:34:18,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6a3e68-3372-4761-a64c-d2018dc930e3/GCF_016881405.1_ASM1688140v1_genomic.fna.gz --refList GCF_016881405.1_ASM1688140v1_genomic.fna/target_genomes.txt --output GCF_016881405.1_ASM1688140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:30,694] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:30,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:30,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:30,702] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:30,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:30,702] [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
Deefgea chitinilytica	strain=LMG 24817	GCA_016881405.1	570276	570276	type	True	100.0	1123	1123	95	conclusive
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	81.2282	692	1123	95	below_threshold
Deefgea salmonis	strain=H3-26	GCA_020531905.1	2875502	2875502	type	True	79.6285	527	1123	95	below_threshold
Chitinibacter bivalviorum	strain=2T18	GCA_013403565.1	2739434	2739434	type	True	78.9659	352	1123	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	78.4877	346	1123	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	78.0129	259	1123	95	below_threshold
Iodobacter fluviatilis	strain=NCTC11159	GCA_900451195.1	537	537	type	True	76.7863	131	1123	95	below_threshold
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	76.6495	57	1123	95	below_threshold
Iodobacter fluviatilis	strain=DSM 3764	GCA_004346505.1	537	537	type	True	76.6465	131	1123	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	75.7792	75	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:30,704] [INFO] DFAST Taxonomy check result was written to GCF_016881405.1_ASM1688140v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:30,705] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:30,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:30,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference/checkm_data
[2024-01-25 17:34:30,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:30,741] [INFO] Task started: CheckM
[2024-01-25 17:34:30,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016881405.1_ASM1688140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016881405.1_ASM1688140v1_genomic.fna/checkm_input GCF_016881405.1_ASM1688140v1_genomic.fna/checkm_result
[2024-01-25 17:34:59,131] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:59,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:59,151] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:59,151] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:59,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016881405.1_ASM1688140v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:59,151] [INFO] Task started: Blastn
[2024-01-25 17:34:59,152] [INFO] Running command: blastn -query GCF_016881405.1_ASM1688140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd7e46c1-d1ee-48d9-af20-b4140cefd09b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016881405.1_ASM1688140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:00,249] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:00,252] [INFO] Selected 11 target genomes.
[2024-01-25 17:35:00,252] [INFO] Target genome list was writen to GCF_016881405.1_ASM1688140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:00,258] [INFO] Task started: fastANI
[2024-01-25 17:35:00,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6a3e68-3372-4761-a64c-d2018dc930e3/GCF_016881405.1_ASM1688140v1_genomic.fna.gz --refList GCF_016881405.1_ASM1688140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016881405.1_ASM1688140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:08,311] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:08,318] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:08,318] [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_016881405.1	s__Deefgea chitinilytica	100.0	1123	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000620145.1	s__Deefgea rivuli	81.2106	695	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284055.1	s__Deefgea sp013284055	79.7755	525	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	95.22	95.22	0.87	0.87	2	-
GCF_013403565.1	s__Chitinibacter sp013403565	78.9785	351	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760905.1	s__Chitinibacter sp009760905	78.8304	312	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423785.1	s__Chitinibacter fontanus	78.4837	347	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429785.1	s__Chitinibacter tainanensis	78.0164	257	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	96.34	96.34	0.90	0.90	2	-
GCF_000969645.2	s__Iodobacter sp000969645	76.845	130	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451195.1	s__Iodobacter fluviatilis	76.7712	133	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000711875.1	s__Andreprevotia chitinilytica	76.6495	57	1123	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430805.1	s__Chitinilyticum aquatile	75.7792	75	1123	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 17:35:08,320] [INFO] GTDB search result was written to GCF_016881405.1_ASM1688140v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:08,321] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:08,323] [INFO] DFAST_QC result json was written to GCF_016881405.1_ASM1688140v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:08,323] [INFO] DFAST_QC completed!
[2024-01-25 17:35:08,323] [INFO] Total running time: 0h1m1s