[2024-01-24 14:28:08,482] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:08,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:08,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference
[2024-01-24 14:28:10,421] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,422] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,423] [INFO] Running command: gunzip -c /var/lib/cwl/stg44a53416-e758-405f-8772-b30c011892b5/GCF_000749905.1_ASM74990v1_genomic.fna.gz | prodigal -d GCF_000749905.1_ASM74990v1_genomic.fna/cds.fna -a GCF_000749905.1_ASM74990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:24,696] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:24,696] [INFO] Task started: HMMsearch
[2024-01-24 14:28:24,697] [INFO] Running command: hmmsearch --tblout GCF_000749905.1_ASM74990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference/reference_markers.hmm GCF_000749905.1_ASM74990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:25,025] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:25,026] [INFO] Found 6/6 markers.
[2024-01-24 14:28:25,069] [INFO] Query marker FASTA was written to GCF_000749905.1_ASM74990v1_genomic.fna/markers.fasta
[2024-01-24 14:28:25,070] [INFO] Task started: Blastn
[2024-01-24 14:28:25,070] [INFO] Running command: blastn -query GCF_000749905.1_ASM74990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference/reference_markers.fasta -out GCF_000749905.1_ASM74990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:25,991] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:25,996] [INFO] Selected 17 target genomes.
[2024-01-24 14:28:25,997] [INFO] Target genome list was writen to GCF_000749905.1_ASM74990v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:26,011] [INFO] Task started: fastANI
[2024-01-24 14:28:26,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg44a53416-e758-405f-8772-b30c011892b5/GCF_000749905.1_ASM74990v1_genomic.fna.gz --refList GCF_000749905.1_ASM74990v1_genomic.fna/target_genomes.txt --output GCF_000749905.1_ASM74990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:46,806] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:46,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:46,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:46,831] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:46,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:46,832] [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
Pectobacterium atrosepticum	strain=NCPPB 549	GCA_000749905.1	29471	29471	type	True	100.0	1679	1682	95	conclusive
Pectobacterium atrosepticum	strain=ICMP 1526	GCA_001038685.1	29471	29471	type	True	99.9851	1596	1682	95	conclusive
Pectobacterium peruviense	strain=IFB5232	GCA_002847345.1	2066479	2066479	type	True	93.8672	1425	1682	95	below_threshold
Pectobacterium betavasculorum	strain=NCPPB 2795	GCA_000749845.1	55207	55207	type	True	92.0817	1271	1682	95	below_threshold
Pectobacterium zantedeschiae	strain=9M	GCA_004137795.1	2034769	2034769	type	True	91.3207	1358	1682	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	89.9815	1277	1682	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	89.9788	1297	1682	95	below_threshold
Pectobacterium parvum	strain=s0421	GCA_900195285.2	2778550	2778550	type	True	89.83	1234	1682	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	89.8289	1336	1682	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_001742145.1	1905730	1905730	type	True	89.8149	1298	1682	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	89.3217	1201	1682	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.5507	1292	1682	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7086	372	1682	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.4501	366	1682	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.3041	358	1682	95	below_threshold
Aliagarivorans marinus	strain=DSM 23064	GCA_000429485.1	561965	561965	type	True	76.1834	53	1682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:46,833] [INFO] DFAST Taxonomy check result was written to GCF_000749905.1_ASM74990v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:46,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:46,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:46,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference/checkm_data
[2024-01-24 14:28:46,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:46,894] [INFO] Task started: CheckM
[2024-01-24 14:28:46,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000749905.1_ASM74990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000749905.1_ASM74990v1_genomic.fna/checkm_input GCF_000749905.1_ASM74990v1_genomic.fna/checkm_result
[2024-01-24 14:29:33,647] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:33,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:33,667] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:33,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:33,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000749905.1_ASM74990v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:33,668] [INFO] Task started: Blastn
[2024-01-24 14:29:33,668] [INFO] Running command: blastn -query GCF_000749905.1_ASM74990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31ffe151-4e77-43f8-9f81-2986c270ed1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000749905.1_ASM74990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:34,823] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:34,827] [INFO] Selected 13 target genomes.
[2024-01-24 14:29:34,827] [INFO] Target genome list was writen to GCF_000749905.1_ASM74990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:34,842] [INFO] Task started: fastANI
[2024-01-24 14:29:34,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg44a53416-e758-405f-8772-b30c011892b5/GCF_000749905.1_ASM74990v1_genomic.fna.gz --refList GCF_000749905.1_ASM74990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000749905.1_ASM74990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:51,215] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:51,234] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:51,235] [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_019056595.1	s__Pectobacterium atrosepticum	99.9809	1651	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.44	98.81	0.97	0.94	14	conclusive
GCF_002847345.1	s__Pectobacterium peruviense	93.8672	1425	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.76	97.64	0.96	0.93	5	-
GCF_000749845.1	s__Pectobacterium betavasculorum	92.0937	1270	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.45	99.45	0.94	0.94	2	-
GCF_004137795.1	s__Pectobacterium zantedeschiae	91.3207	1358	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.24	98.49	0.92	0.91	3	-
GCF_001742185.1	s__Pectobacterium wasabiae	89.977	1297	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.99	99.99	0.99	0.98	4	-
GCF_900129615.1	s__Pectobacterium carotovorum	89.9277	1318	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.11	95.19	0.90	0.85	81	-
GCF_001742145.1	s__Pectobacterium parmentieri	89.8352	1296	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.20	98.87	0.95	0.90	33	-
GCF_002307355.1	s__Pectobacterium polaris	89.8289	1336	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.45	95.13	0.88	0.82	21	-
GCF_000754695.1	s__Pectobacterium brasiliense	89.7024	1343	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	96.37	95.20	0.89	0.82	92	-
GCF_012427845.1	s__Pectobacterium punjabense	89.5923	1301	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	99.35	98.67	0.97	0.93	5	-
GCF_005497185.1	s__Pectobacterium polonicum	89.5313	1315	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382565.2	s__Pectobacterium aquaticum	89.4232	1170	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	97.07	95.76	0.89	0.87	15	-
GCF_013449685.1	s__Pectobacterium brasiliense_A	89.2647	1250	1682	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium	95.0	98.47	96.08	0.92	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:51,236] [INFO] GTDB search result was written to GCF_000749905.1_ASM74990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:51,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:51,242] [INFO] DFAST_QC result json was written to GCF_000749905.1_ASM74990v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:51,242] [INFO] DFAST_QC completed!
[2024-01-24 14:29:51,242] [INFO] Total running time: 0h1m43s