[2024-01-24 12:06:13,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,870] [INFO] DQC Reference Directory: /var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference
[2024-01-24 12:06:15,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,243] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e69e11b-6fc2-4815-9455-cb86cd5b2782/GCF_001038685.1_ASM103868v1_genomic.fna.gz | prodigal -d GCF_001038685.1_ASM103868v1_genomic.fna/cds.fna -a GCF_001038685.1_ASM103868v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:28,712] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:28,713] [INFO] Task started: HMMsearch
[2024-01-24 12:06:28,713] [INFO] Running command: hmmsearch --tblout GCF_001038685.1_ASM103868v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference/reference_markers.hmm GCF_001038685.1_ASM103868v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:29,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:29,049] [INFO] Found 6/6 markers.
[2024-01-24 12:06:29,103] [INFO] Query marker FASTA was written to GCF_001038685.1_ASM103868v1_genomic.fna/markers.fasta
[2024-01-24 12:06:29,104] [INFO] Task started: Blastn
[2024-01-24 12:06:29,104] [INFO] Running command: blastn -query GCF_001038685.1_ASM103868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference/reference_markers.fasta -out GCF_001038685.1_ASM103868v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,031] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,034] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:30,034] [INFO] Target genome list was writen to GCF_001038685.1_ASM103868v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,041] [INFO] Task started: fastANI
[2024-01-24 12:06:30,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e69e11b-6fc2-4815-9455-cb86cd5b2782/GCF_001038685.1_ASM103868v1_genomic.fna.gz --refList GCF_001038685.1_ASM103868v1_genomic.fna/target_genomes.txt --output GCF_001038685.1_ASM103868v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:47,584] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:47,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:47,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:47,598] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:47,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:47,599] [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=ICMP 1526	GCA_001038685.1	29471	29471	type	True	100.0	1607	1611	95	conclusive
Pectobacterium atrosepticum	strain=NCPPB 549	GCA_000749905.1	29471	29471	type	True	99.9864	1591	1611	95	conclusive
Pectobacterium peruviense	strain=IFB5232	GCA_002847345.1	2066479	2066479	type	True	93.9295	1357	1611	95	below_threshold
Pectobacterium betavasculorum	strain=NCPPB 2795	GCA_000749845.1	55207	55207	type	True	92.0795	1204	1611	95	below_threshold
Pectobacterium zantedeschiae	strain=9M	GCA_004137795.1	2034769	2034769	type	True	91.333	1283	1611	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_000291725.1	55208	55208	type	True	90.0572	1209	1611	95	below_threshold
Pectobacterium wasabiae	strain=CFBP 3304	GCA_001742185.1	55208	55208	type	True	90.0316	1230	1611	95	below_threshold
Pectobacterium parmentieri	strain=RNS 08-42-1A	GCA_001742145.1	1905730	1905730	type	True	89.8303	1235	1611	95	below_threshold
Pectobacterium polaris	strain=NIBIO1006	GCA_002307355.1	2042057	2042057	type	True	89.7961	1276	1611	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	89.3729	1145	1611	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	88.5127	1231	1611	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7054	357	1611	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.3356	362	1611	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.323	341	1611	95	below_threshold
Aliagarivorans marinus	strain=DSM 23064	GCA_000429485.1	561965	561965	type	True	76.2523	50	1611	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:47,601] [INFO] DFAST Taxonomy check result was written to GCF_001038685.1_ASM103868v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:47,601] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:47,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:47,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference/checkm_data
[2024-01-24 12:06:47,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:47,658] [INFO] Task started: CheckM
[2024-01-24 12:06:47,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001038685.1_ASM103868v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001038685.1_ASM103868v1_genomic.fna/checkm_input GCF_001038685.1_ASM103868v1_genomic.fna/checkm_result
[2024-01-24 12:07:29,920] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:29,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:29,944] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:29,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:29,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001038685.1_ASM103868v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:29,945] [INFO] Task started: Blastn
[2024-01-24 12:07:29,945] [INFO] Running command: blastn -query GCF_001038685.1_ASM103868v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf927bbc2-89a4-40ec-92e4-2f5ce37ee223/dqc_reference/reference_markers_gtdb.fasta -out GCF_001038685.1_ASM103868v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:31,325] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:31,330] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:31,330] [INFO] Target genome list was writen to GCF_001038685.1_ASM103868v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:31,347] [INFO] Task started: fastANI
[2024-01-24 12:07:31,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e69e11b-6fc2-4815-9455-cb86cd5b2782/GCF_001038685.1_ASM103868v1_genomic.fna.gz --refList GCF_001038685.1_ASM103868v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001038685.1_ASM103868v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:47,038] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:47,055] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:47,055] [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	99.9764	1587	1611	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	93.9295	1357	1611	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	92.0861	1203	1611	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	91.333	1283	1611	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	89.9936	1233	1611	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	89.9466	1246	1611	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	89.8392	1235	1611	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	89.7961	1276	1611	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	89.7082	1271	1611	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	89.5568	1229	1611	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	89.4777	1256	1611	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	89.425	1126	1611	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	89.2916	1182	1611	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 12:07:47,056] [INFO] GTDB search result was written to GCF_001038685.1_ASM103868v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:47,057] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:47,060] [INFO] DFAST_QC result json was written to GCF_001038685.1_ASM103868v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:47,061] [INFO] DFAST_QC completed!
[2024-01-24 12:07:47,061] [INFO] Total running time: 0h1m33s