[2024-01-24 13:31:44,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference
[2024-01-24 13:31:45,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,732] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg48759c3f-4188-46ae-9726-a7e47f0f44a5/GCF_003201855.1_ASM320185v1_genomic.fna.gz | prodigal -d GCF_003201855.1_ASM320185v1_genomic.fna/cds.fna -a GCF_003201855.1_ASM320185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:58,190] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:58,191] [INFO] Task started: HMMsearch
[2024-01-24 13:31:58,191] [INFO] Running command: hmmsearch --tblout GCF_003201855.1_ASM320185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference/reference_markers.hmm GCF_003201855.1_ASM320185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:58,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:58,501] [INFO] Found 6/6 markers.
[2024-01-24 13:31:58,549] [INFO] Query marker FASTA was written to GCF_003201855.1_ASM320185v1_genomic.fna/markers.fasta
[2024-01-24 13:31:58,549] [INFO] Task started: Blastn
[2024-01-24 13:31:58,549] [INFO] Running command: blastn -query GCF_003201855.1_ASM320185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference/reference_markers.fasta -out GCF_003201855.1_ASM320185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:59,629] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:59,633] [INFO] Selected 21 target genomes.
[2024-01-24 13:31:59,633] [INFO] Target genome list was writen to GCF_003201855.1_ASM320185v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:59,641] [INFO] Task started: fastANI
[2024-01-24 13:31:59,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg48759c3f-4188-46ae-9726-a7e47f0f44a5/GCF_003201855.1_ASM320185v1_genomic.fna.gz --refList GCF_003201855.1_ASM320185v1_genomic.fna/target_genomes.txt --output GCF_003201855.1_ASM320185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:16,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:16,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:16,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:16,545] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:16,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:16,545] [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
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	100.0	1204	1209	95	conclusive
Chromobacterium paludis	strain=IIBBL 257-1	GCA_008275125.1	2605945	2605945	type	True	79.0003	390	1209	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	78.8998	379	1209	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	78.7877	383	1209	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	78.7866	394	1209	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	78.757	376	1209	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	78.7302	366	1209	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	78.7278	432	1209	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	78.716	387	1209	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	78.637	432	1209	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	78.6184	428	1209	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	78.5795	391	1209	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	78.5624	412	1209	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.5299	342	1209	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	78.5002	414	1209	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	78.4837	313	1209	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	78.4712	428	1209	95	below_threshold
Aquitalea denitrificans	strain=5YN1-3	GCA_009856625.1	519081	519081	type	True	78.4613	342	1209	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	78.4296	302	1209	95	below_threshold
Aquitalea aquatilis	strain=THG-DN7.12	GCA_005155025.1	1537400	1537400	type	True	78.285	389	1209	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	76.6783	109	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,547] [INFO] DFAST Taxonomy check result was written to GCF_003201855.1_ASM320185v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:16,548] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:16,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:16,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference/checkm_data
[2024-01-24 13:32:16,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:16,592] [INFO] Task started: CheckM
[2024-01-24 13:32:16,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003201855.1_ASM320185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003201855.1_ASM320185v1_genomic.fna/checkm_input GCF_003201855.1_ASM320185v1_genomic.fna/checkm_result
[2024-01-24 13:32:57,297] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:57,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,317] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:57,317] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:57,318] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003201855.1_ASM320185v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:57,319] [INFO] Task started: Blastn
[2024-01-24 13:32:57,319] [INFO] Running command: blastn -query GCF_003201855.1_ASM320185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d350261-eb56-4f44-9064-72b1d075a987/dqc_reference/reference_markers_gtdb.fasta -out GCF_003201855.1_ASM320185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:59,077] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:59,081] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:59,081] [INFO] Target genome list was writen to GCF_003201855.1_ASM320185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:59,096] [INFO] Task started: fastANI
[2024-01-24 13:32:59,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg48759c3f-4188-46ae-9726-a7e47f0f44a5/GCF_003201855.1_ASM320185v1_genomic.fna.gz --refList GCF_003201855.1_ASM320185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003201855.1_ASM320185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:15,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:15,797] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:15,797] [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_003201855.1	s__Rivicola pingtungensis	100.0	1204	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002002905.1	s__Rivicola sp002002905	85.3587	904	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Rivicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090205.1	s__Vogesella sp900090205	79.1048	418	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527175.1	s__Pseudogulbenkiania sp000527175	79.0214	383	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002213445.1	s__Chromobacterium sp002213445	79.0191	402	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	99.12	0.94	0.94	2	-
GCF_008275125.1	s__Chromobacterium paludis	78.9837	391	1209	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	78.9333	378	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_016937655.1	s__Chromobacterium alkanivorans	78.9265	432	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.67	98.67	0.95	0.95	2	-
GCF_001855565.1	s__Chromobacterium amazonense	78.894	379	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_002924365.1	s__Chromobacterium sp002924365	78.7769	384	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652475.1	s__Vogesella alkaliphila	78.7752	395	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676875.1	s__Chromobacterium subtsugae	78.7174	432	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_003325475.1	s__Chromobacterium phragmitis	78.5108	416	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_009856625.1	s__Aquitalea denitrificans	78.4552	343	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423285.1	s__Laribacter hongkongensis	78.4497	308	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Laribacter	95.0	98.14	97.82	0.92	0.90	5	-
GCF_000620105.1	s__Microvirgula aerodenitrificans	78.3766	355	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Aquaspirillaceae;g__Microvirgula	95.0	99.13	99.12	0.93	0.93	3	-
GCA_016192025.1	s__Pseudogulbenkiania sp016192025	78.3529	309	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005155025.1	s__Aquitalea aquatilis	78.255	392	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	99.19	99.19	0.95	0.95	2	-
GCA_017989485.1	s__JAGNPU01 sp017989485	75.8186	53	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:15,799] [INFO] GTDB search result was written to GCF_003201855.1_ASM320185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:15,799] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:15,811] [INFO] DFAST_QC result json was written to GCF_003201855.1_ASM320185v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:15,811] [INFO] DFAST_QC completed!
[2024-01-24 13:33:15,811] [INFO] Total running time: 0h1m31s