[2024-01-24 13:58:25,768] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference
[2024-01-24 13:58:27,137] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:27,138] [INFO] Task started: Prodigal
[2024-01-24 13:58:27,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg236273fa-dcdf-42bd-8519-ff8f3eb5ff87/GCF_019665765.1_ASM1966576v1_genomic.fna.gz | prodigal -d GCF_019665765.1_ASM1966576v1_genomic.fna/cds.fna -a GCF_019665765.1_ASM1966576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:39,535] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:39,536] [INFO] Task started: HMMsearch
[2024-01-24 13:58:39,536] [INFO] Running command: hmmsearch --tblout GCF_019665765.1_ASM1966576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference/reference_markers.hmm GCF_019665765.1_ASM1966576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:39,855] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:39,856] [INFO] Found 6/6 markers.
[2024-01-24 13:58:39,891] [INFO] Query marker FASTA was written to GCF_019665765.1_ASM1966576v1_genomic.fna/markers.fasta
[2024-01-24 13:58:39,891] [INFO] Task started: Blastn
[2024-01-24 13:58:39,891] [INFO] Running command: blastn -query GCF_019665765.1_ASM1966576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference/reference_markers.fasta -out GCF_019665765.1_ASM1966576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:40,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:40,636] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:40,636] [INFO] Target genome list was writen to GCF_019665765.1_ASM1966576v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:40,663] [INFO] Task started: fastANI
[2024-01-24 13:58:40,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg236273fa-dcdf-42bd-8519-ff8f3eb5ff87/GCF_019665765.1_ASM1966576v1_genomic.fna.gz --refList GCF_019665765.1_ASM1966576v1_genomic.fna/target_genomes.txt --output GCF_019665765.1_ASM1966576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:52,437] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:52,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:52,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:52,447] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:52,447] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:52,447] [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	83.5696	825	1185	95	below_threshold
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	81.8546	745	1185	95	below_threshold
Deefgea salmonis	strain=H3-26	GCA_020531905.1	2875502	2875502	type	True	80.0978	553	1185	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	78.9152	332	1185	95	below_threshold
Chitinibacter bivalviorum	strain=2T18	GCA_013403565.1	2739434	2739434	type	True	78.6901	384	1185	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	77.8583	240	1185	95	below_threshold
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	76.6275	52	1185	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	76.5782	55	1185	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	75.8756	67	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,449] [INFO] DFAST Taxonomy check result was written to GCF_019665765.1_ASM1966576v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:52,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:52,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:52,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference/checkm_data
[2024-01-24 13:58:52,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:52,487] [INFO] Task started: CheckM
[2024-01-24 13:58:52,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019665765.1_ASM1966576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019665765.1_ASM1966576v1_genomic.fna/checkm_input GCF_019665765.1_ASM1966576v1_genomic.fna/checkm_result
[2024-01-24 13:59:35,436] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:35,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:35,454] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:35,454] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:35,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019665765.1_ASM1966576v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:35,455] [INFO] Task started: Blastn
[2024-01-24 13:59:35,456] [INFO] Running command: blastn -query GCF_019665765.1_ASM1966576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a583b62-47ce-406e-9d8e-043a82eb7fd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019665765.1_ASM1966576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:36,535] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:36,538] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:36,538] [INFO] Target genome list was writen to GCF_019665765.1_ASM1966576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:36,553] [INFO] Task started: fastANI
[2024-01-24 13:59:36,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg236273fa-dcdf-42bd-8519-ff8f3eb5ff87/GCF_019665765.1_ASM1966576v1_genomic.fna.gz --refList GCF_019665765.1_ASM1966576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019665765.1_ASM1966576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:45,538] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:45,553] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:45,553] [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	83.5696	825	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000620145.1	s__Deefgea rivuli	81.845	746	1185	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	80.8038	553	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	95.22	95.22	0.87	0.87	2	-
GCF_013423785.1	s__Chitinibacter fontanus	78.7919	334	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403565.1	s__Chitinibacter sp013403565	78.6949	385	1185	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	78.4954	322	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004194535.1	s__Iodobacter fluviatilis_A	78.1621	155	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429785.1	s__Chitinibacter tainanensis	77.855	239	1185	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	77.763	158	1185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223195.1	s__Chitinilyticum litopenaei_A	76.539	56	1185	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	75.8764	67	1185	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 13:59:45,555] [INFO] GTDB search result was written to GCF_019665765.1_ASM1966576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:45,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:45,560] [INFO] DFAST_QC result json was written to GCF_019665765.1_ASM1966576v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:45,561] [INFO] DFAST_QC completed!
[2024-01-24 13:59:45,561] [INFO] Total running time: 0h1m20s