[2024-01-24 12:31:51,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference
[2024-01-24 12:31:52,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,578] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg12e560b4-95b6-43a5-8b00-cd964c23dfb6/GCF_000422925.1_ASM42292v1_genomic.fna.gz | prodigal -d GCF_000422925.1_ASM42292v1_genomic.fna/cds.fna -a GCF_000422925.1_ASM42292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:05,621] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:05,622] [INFO] Task started: HMMsearch
[2024-01-24 12:32:05,622] [INFO] Running command: hmmsearch --tblout GCF_000422925.1_ASM42292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference/reference_markers.hmm GCF_000422925.1_ASM42292v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:05,904] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:05,906] [INFO] Found 6/6 markers.
[2024-01-24 12:32:05,951] [INFO] Query marker FASTA was written to GCF_000422925.1_ASM42292v1_genomic.fna/markers.fasta
[2024-01-24 12:32:05,951] [INFO] Task started: Blastn
[2024-01-24 12:32:05,951] [INFO] Running command: blastn -query GCF_000422925.1_ASM42292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference/reference_markers.fasta -out GCF_000422925.1_ASM42292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:06,898] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:06,902] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:06,903] [INFO] Target genome list was writen to GCF_000422925.1_ASM42292v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:06,917] [INFO] Task started: fastANI
[2024-01-24 12:32:06,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg12e560b4-95b6-43a5-8b00-cd964c23dfb6/GCF_000422925.1_ASM42292v1_genomic.fna.gz --refList GCF_000422925.1_ASM42292v1_genomic.fna/target_genomes.txt --output GCF_000422925.1_ASM42292v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:19,458] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:19,459] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:19,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:19,477] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:19,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:19,478] [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
Paludibacterium yongneupense	strain=DSM 18731	GCA_000422925.1	400061	400061	type	True	100.0	1416	1420	95	conclusive
Paludibacterium paludis	strain=KCTC 32182	GCA_014652495.1	1225769	1225769	type	True	78.619	341	1420	95	below_threshold
Paludibacterium purpuratum	strain=CECT 8976	GCA_004363805.1	1144873	1144873	type	True	78.5568	357	1420	95	below_threshold
Paludibacterium paludis	strain=BCRC 80514	GCA_018802605.1	1225769	1225769	type	True	78.5383	346	1420	95	below_threshold
Chromobacterium alkanivorans	strain=IITR-71	GCA_016937655.1	1071719	1071719	type	True	78.4962	403	1420	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.4594	395	1420	95	below_threshold
Crenobacter cavernae	strain=K1W11S-77	GCA_003355495.1	2290923	2290923	type	True	78.3513	315	1420	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	78.3205	389	1420	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.2788	379	1420	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	78.2427	318	1420	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	78.239	373	1420	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.2329	397	1420	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.1773	384	1420	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	78.0297	315	1420	95	below_threshold
Gulbenkiania indica	strain=DSM 17901	GCA_001418035.1	375574	375574	type	True	77.7485	239	1420	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	77.335	213	1420	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	75.7895	65	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:19,480] [INFO] DFAST Taxonomy check result was written to GCF_000422925.1_ASM42292v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:19,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:19,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:19,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference/checkm_data
[2024-01-24 12:32:19,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:19,528] [INFO] Task started: CheckM
[2024-01-24 12:32:19,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422925.1_ASM42292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422925.1_ASM42292v1_genomic.fna/checkm_input GCF_000422925.1_ASM42292v1_genomic.fna/checkm_result
[2024-01-24 12:32:59,339] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:59,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:59,369] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:59,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:59,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422925.1_ASM42292v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:59,371] [INFO] Task started: Blastn
[2024-01-24 12:32:59,371] [INFO] Running command: blastn -query GCF_000422925.1_ASM42292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9efe6e84-2308-461f-a24f-6be55b0c72bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422925.1_ASM42292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:01,159] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:01,163] [INFO] Selected 18 target genomes.
[2024-01-24 12:33:01,164] [INFO] Target genome list was writen to GCF_000422925.1_ASM42292v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:01,183] [INFO] Task started: fastANI
[2024-01-24 12:33:01,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg12e560b4-95b6-43a5-8b00-cd964c23dfb6/GCF_000422925.1_ASM42292v1_genomic.fna.gz --refList GCF_000422925.1_ASM42292v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422925.1_ASM42292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:14,613] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:14,630] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:14,630] [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_000422925.1	s__Paludibacterium yongneupense	100.0	1416	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	78.8015	376	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363805.1	s__Paludibacterium purpuratum	78.572	357	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018802765.1	s__Paludibacterium sp018802765	78.5712	375	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018802605.1	s__Paludibacterium paludis	78.5428	345	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002848345.1	s__Chromobacterium sp002848345	78.5171	407	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002213445.1	s__Chromobacterium sp002213445	78.4997	397	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_000174355.1	s__Pseudogulbenkiania ferrooxidans_A	78.4954	368	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	97.29	97.29	0.89	0.89	2	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	78.3844	374	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232825.1	s__Paludibacterium sp019232825	78.3419	389	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Paludibacterium	95.0	99.73	99.73	0.94	0.94	2	-
GCF_003355495.1	s__Crenobacter cavernae	78.3401	316	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Crenobacter	95.0	96.17	96.17	0.93	0.93	2	-
GCF_002924365.1	s__Chromobacterium sp002924365	78.2781	380	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428945.1	s__Chromobacterium sp016428945	78.2374	390	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_001855565.1	s__Chromobacterium amazonense	78.1748	382	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_001676875.1	s__Chromobacterium subtsugae	78.1714	394	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_014652335.1	s__Vogesella fluminis	77.9949	317	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217795.2	s__Aquitalea magnusonii_B	77.6432	334	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003856275.1	s__STGJ01 sp003856275	77.6089	251	1420	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__STGJ01	95.0	97.91	97.91	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:14,631] [INFO] GTDB search result was written to GCF_000422925.1_ASM42292v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:14,632] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:14,638] [INFO] DFAST_QC result json was written to GCF_000422925.1_ASM42292v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:14,638] [INFO] DFAST_QC completed!
[2024-01-24 12:33:14,638] [INFO] Total running time: 0h1m23s