[2024-01-24 13:17:14,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,005] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference
[2024-01-24 13:17:15,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,306] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg49fdea61-5c06-4336-be29-e38fb14d88d9/GCF_000428465.1_ASM42846v1_genomic.fna.gz | prodigal -d GCF_000428465.1_ASM42846v1_genomic.fna/cds.fna -a GCF_000428465.1_ASM42846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:32,960] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:32,960] [INFO] Task started: HMMsearch
[2024-01-24 13:17:32,960] [INFO] Running command: hmmsearch --tblout GCF_000428465.1_ASM42846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference/reference_markers.hmm GCF_000428465.1_ASM42846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,295] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,297] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,344] [INFO] Query marker FASTA was written to GCF_000428465.1_ASM42846v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,344] [INFO] Task started: Blastn
[2024-01-24 13:17:33,344] [INFO] Running command: blastn -query GCF_000428465.1_ASM42846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference/reference_markers.fasta -out GCF_000428465.1_ASM42846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,333] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,338] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:34,339] [INFO] Target genome list was writen to GCF_000428465.1_ASM42846v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,347] [INFO] Task started: fastANI
[2024-01-24 13:17:34,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg49fdea61-5c06-4336-be29-e38fb14d88d9/GCF_000428465.1_ASM42846v1_genomic.fna.gz --refList GCF_000428465.1_ASM42846v1_genomic.fna/target_genomes.txt --output GCF_000428465.1_ASM42846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:52,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:52,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:52,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:52,885] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:52,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:52,885] [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	100.0	1841	1845	95	conclusive
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	80.3427	799	1845	95	below_threshold
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	79.448	699	1845	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	79.2797	592	1845	95	below_threshold
Chitiniphilus shinanonensis	strain=DSM 23277	GCA_000374805.1	553088	553088	type	True	79.132	650	1845	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	78.8833	524	1845	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	78.8694	507	1845	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	78.4751	508	1845	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	78.3256	485	1845	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	77.9082	430	1845	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.6756	513	1845	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	77.1573	431	1845	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	77.1331	526	1845	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.8172	675	1845	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	76.4838	498	1845	95	below_threshold
Paraburkholderia haematera	strain=LMG 31837	GCA_905220975.1	2793077	2793077	type	True	76.0464	258	1845	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:52,887] [INFO] DFAST Taxonomy check result was written to GCF_000428465.1_ASM42846v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:52,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:52,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:52,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference/checkm_data
[2024-01-24 13:17:52,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:52,944] [INFO] Task started: CheckM
[2024-01-24 13:17:52,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000428465.1_ASM42846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000428465.1_ASM42846v1_genomic.fna/checkm_input GCF_000428465.1_ASM42846v1_genomic.fna/checkm_result
[2024-01-24 13:18:45,397] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:45,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:45,420] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:45,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:45,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000428465.1_ASM42846v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:45,421] [INFO] Task started: Blastn
[2024-01-24 13:18:45,422] [INFO] Running command: blastn -query GCF_000428465.1_ASM42846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f748e92-ea0e-4515-9f11-821c45ba0692/dqc_reference/reference_markers_gtdb.fasta -out GCF_000428465.1_ASM42846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:47,337] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:47,342] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:47,342] [INFO] Target genome list was writen to GCF_000428465.1_ASM42846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:47,358] [INFO] Task started: fastANI
[2024-01-24 13:18:47,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg49fdea61-5c06-4336-be29-e38fb14d88d9/GCF_000428465.1_ASM42846v1_genomic.fna.gz --refList GCF_000428465.1_ASM42846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000428465.1_ASM42846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:04,214] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:04,237] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:04,237] [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	100.0	1841	1845	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	80.3495	797	1845	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	79.4764	695	1845	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	79.2389	597	1845	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	79.1414	428	1845	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	79.0431	660	1845	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	78.9114	520	1845	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	78.7951	569	1845	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	78.5092	539	1845	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	78.4436	513	1845	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	77.9125	431	1845	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	77.6435	519	1845	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	77.1651	468	1845	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	76.3232	333	1845	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	76.2935	302	1845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__CAIKXV01;g__CAIKXV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:04,239] [INFO] GTDB search result was written to GCF_000428465.1_ASM42846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:04,239] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:04,243] [INFO] DFAST_QC result json was written to GCF_000428465.1_ASM42846v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:04,243] [INFO] DFAST_QC completed!
[2024-01-24 13:19:04,243] [INFO] Total running time: 0h1m50s