[2024-01-25 18:42:50,749] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:50,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:50,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference
[2024-01-25 18:42:52,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:52,007] [INFO] Task started: Prodigal
[2024-01-25 18:42:52,007] [INFO] Running command: gunzip -c /var/lib/cwl/stgf74cad08-5bff-47f7-9b1f-03e5f8f6ee76/GCF_014353015.1_ASM1435301v1_genomic.fna.gz | prodigal -d GCF_014353015.1_ASM1435301v1_genomic.fna/cds.fna -a GCF_014353015.1_ASM1435301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:11,136] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:11,136] [INFO] Task started: HMMsearch
[2024-01-25 18:43:11,136] [INFO] Running command: hmmsearch --tblout GCF_014353015.1_ASM1435301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference/reference_markers.hmm GCF_014353015.1_ASM1435301v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:11,478] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:11,479] [INFO] Found 6/6 markers.
[2024-01-25 18:43:11,527] [INFO] Query marker FASTA was written to GCF_014353015.1_ASM1435301v1_genomic.fna/markers.fasta
[2024-01-25 18:43:11,527] [INFO] Task started: Blastn
[2024-01-25 18:43:11,527] [INFO] Running command: blastn -query GCF_014353015.1_ASM1435301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference/reference_markers.fasta -out GCF_014353015.1_ASM1435301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:12,460] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:12,466] [INFO] Selected 16 target genomes.
[2024-01-25 18:43:12,467] [INFO] Target genome list was writen to GCF_014353015.1_ASM1435301v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:12,476] [INFO] Task started: fastANI
[2024-01-25 18:43:12,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgf74cad08-5bff-47f7-9b1f-03e5f8f6ee76/GCF_014353015.1_ASM1435301v1_genomic.fna.gz --refList GCF_014353015.1_ASM1435301v1_genomic.fna/target_genomes.txt --output GCF_014353015.1_ASM1435301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:30,944] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:30,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:30,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:30,956] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:30,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:30,956] [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
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	99.93	1838	1882	95	conclusive
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	80.4395	777	1882	95	below_threshold
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	79.44	722	1882	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	79.3625	584	1882	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	79.0572	679	1882	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	79.0363	528	1882	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	78.8786	505	1882	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	78.4891	517	1882	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	78.4372	479	1882	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.917	444	1882	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.7261	508	1882	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.1737	439	1882	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.11	537	1882	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7564	714	1882	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	76.355	532	1882	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	75.9874	280	1882	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:30,958] [INFO] DFAST Taxonomy check result was written to GCF_014353015.1_ASM1435301v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:30,958] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:30,959] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:30,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference/checkm_data
[2024-01-25 18:43:30,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:31,016] [INFO] Task started: CheckM
[2024-01-25 18:43:31,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014353015.1_ASM1435301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014353015.1_ASM1435301v1_genomic.fna/checkm_input GCF_014353015.1_ASM1435301v1_genomic.fna/checkm_result
[2024-01-25 18:44:52,490] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:52,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:52,507] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:52,507] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:52,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014353015.1_ASM1435301v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:52,509] [INFO] Task started: Blastn
[2024-01-25 18:44:52,509] [INFO] Running command: blastn -query GCF_014353015.1_ASM1435301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d1bb74-161d-479a-8c8d-4fed65a48a00/dqc_reference/reference_markers_gtdb.fasta -out GCF_014353015.1_ASM1435301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:54,316] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:54,319] [INFO] Selected 15 target genomes.
[2024-01-25 18:44:54,320] [INFO] Target genome list was writen to GCF_014353015.1_ASM1435301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:54,331] [INFO] Task started: fastANI
[2024-01-25 18:44:54,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgf74cad08-5bff-47f7-9b1f-03e5f8f6ee76/GCF_014353015.1_ASM1435301v1_genomic.fna.gz --refList GCF_014353015.1_ASM1435301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014353015.1_ASM1435301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:12,077] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:12,087] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:12,087] [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_000428465.1	s__Chitinimonas koreensis	99.93	1838	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900119825.1	s__Chitinimonas taiwanensis	80.3927	783	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	96.92	96.91	0.93	0.93	3	-
GCF_007431345.1	s__Chitinimonas arctica	79.479	721	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345725.1	s__Crenobacter luteus	79.4007	579	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	98.88	98.88	0.93	0.93	2	-
GCA_019234745.1	s__JAFAKZ01 sp019234745	79.163	443	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__JAFAKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374805.1	s__Chitiniphilus shinanonensis	79.1132	672	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitiniphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355495.1	s__Crenobacter cavernae	79.0099	531	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	78.9646	574	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033135.1	s__Chitinolyticbacter meiyuanensis	78.5842	559	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinolyticbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652315.1	s__Jeongeupia chitinilytica	78.4612	522	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Jeongeupia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	77.9276	442	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	77.7366	505	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720425.1	s__CAIWHR01 sp016720425	77.2663	470	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__CAIWHR01	95.0	98.60	97.38	0.93	0.90	10	-
GCF_017315705.1	s__Trinickia sp017315705	76.255	352	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873475.1	s__CAIKXV01 sp903873475	76.1374	316	1882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__CAIKXV01;g__CAIKXV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:12,090] [INFO] GTDB search result was written to GCF_014353015.1_ASM1435301v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:12,091] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:12,095] [INFO] DFAST_QC result json was written to GCF_014353015.1_ASM1435301v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:12,095] [INFO] DFAST_QC completed!
[2024-01-25 18:45:12,095] [INFO] Total running time: 0h2m21s