[2023-06-19 01:46:29,209] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:46:29,212] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:46:29,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference
[2023-06-19 01:46:30,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:46:30,407] [INFO] Task started: Prodigal
[2023-06-19 01:46:30,407] [INFO] Running command: gunzip -c /var/lib/cwl/stga870bd00-fa3e-41ad-9d30-58ce6903e15f/GCA_018005035.1_ASM1800503v1_genomic.fna.gz | prodigal -d GCA_018005035.1_ASM1800503v1_genomic.fna/cds.fna -a GCA_018005035.1_ASM1800503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:46:32,888] [INFO] Task succeeded: Prodigal
[2023-06-19 01:46:32,888] [INFO] Task started: HMMsearch
[2023-06-19 01:46:32,889] [INFO] Running command: hmmsearch --tblout GCA_018005035.1_ASM1800503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference/reference_markers.hmm GCA_018005035.1_ASM1800503v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:46:33,019] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:46:33,020] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga870bd00-fa3e-41ad-9d30-58ce6903e15f/GCA_018005035.1_ASM1800503v1_genomic.fna.gz]
[2023-06-19 01:46:33,033] [INFO] Query marker FASTA was written to GCA_018005035.1_ASM1800503v1_genomic.fna/markers.fasta
[2023-06-19 01:46:33,033] [INFO] Task started: Blastn
[2023-06-19 01:46:33,034] [INFO] Running command: blastn -query GCA_018005035.1_ASM1800503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference/reference_markers.fasta -out GCA_018005035.1_ASM1800503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:34,222] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:34,230] [INFO] Selected 11 target genomes.
[2023-06-19 01:46:34,230] [INFO] Target genome list was writen to GCA_018005035.1_ASM1800503v1_genomic.fna/target_genomes.txt
[2023-06-19 01:46:34,233] [INFO] Task started: fastANI
[2023-06-19 01:46:34,234] [INFO] Running command: fastANI --query /var/lib/cwl/stga870bd00-fa3e-41ad-9d30-58ce6903e15f/GCA_018005035.1_ASM1800503v1_genomic.fna.gz --refList GCA_018005035.1_ASM1800503v1_genomic.fna/target_genomes.txt --output GCA_018005035.1_ASM1800503v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:46:42,535] [INFO] Task succeeded: fastANI
[2023-06-19 01:46:42,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:46:42,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:46:42,547] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:46:42,547] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:46:42,547] [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
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	80.0926	124	185	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	79.8952	115	185	95	below_threshold
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	79.7775	117	185	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	78.895	94	185	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.8343	90	185	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.6857	84	185	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.4425	92	185	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	78.4233	99	185	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.2862	101	185	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	78.1525	90	185	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	78.1319	71	185	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:46:42,551] [INFO] DFAST Taxonomy check result was written to GCA_018005035.1_ASM1800503v1_genomic.fna/tc_result.tsv
[2023-06-19 01:46:42,553] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:46:42,553] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:46:42,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference/checkm_data
[2023-06-19 01:46:42,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:46:42,567] [INFO] Task started: CheckM
[2023-06-19 01:46:42,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018005035.1_ASM1800503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018005035.1_ASM1800503v1_genomic.fna/checkm_input GCA_018005035.1_ASM1800503v1_genomic.fna/checkm_result
[2023-06-19 01:46:57,272] [INFO] Task succeeded: CheckM
[2023-06-19 01:46:57,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:46:57,299] [INFO] ===== Completeness check finished =====
[2023-06-19 01:46:57,299] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:46:57,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018005035.1_ASM1800503v1_genomic.fna/markers.fasta)
[2023-06-19 01:46:57,300] [INFO] Task started: Blastn
[2023-06-19 01:46:57,300] [INFO] Running command: blastn -query GCA_018005035.1_ASM1800503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74367622-4dc6-47e0-a7d2-765ad8c78c95/dqc_reference/reference_markers_gtdb.fasta -out GCA_018005035.1_ASM1800503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:58,260] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:58,263] [INFO] Selected 13 target genomes.
[2023-06-19 01:46:58,264] [INFO] Target genome list was writen to GCA_018005035.1_ASM1800503v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:46:58,267] [INFO] Task started: fastANI
[2023-06-19 01:46:58,267] [INFO] Running command: fastANI --query /var/lib/cwl/stga870bd00-fa3e-41ad-9d30-58ce6903e15f/GCA_018005035.1_ASM1800503v1_genomic.fna.gz --refList GCA_018005035.1_ASM1800503v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018005035.1_ASM1800503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:47:06,313] [INFO] Task succeeded: fastANI
[2023-06-19 01:47:06,326] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 01:47:06,326] [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
GCA_903941205.1	s__Polaromonas sp903941205	83.3296	154	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116715.1	s__Polaromonas sp900116715	80.4321	123	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103405.1	s__Polaromonas sp900103405	80.3621	127	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711205.1	s__Polaromonas sp003711205	80.2517	129	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000282655.1	s__Polaromonas sp000282655	80.1829	124	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598235.1	s__Polaromonas jejuensis	80.1194	123	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780625.1	s__Polaromonas sp018780625	79.6208	108	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927455.1	s__Polaromonas sp012927455	79.6085	98	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013205645.1	s__Polaromonas sp013205645	79.5553	94	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003415675.1	s__Rhodoferax sp003415675	78.6857	84	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381265.1	s__Curvibacter lanceolatus	78.2862	101	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Curvibacter	95.6079	99.38	99.38	0.94	0.94	2	-
GCF_001424545.1	s__Ramlibacter sp001424545	78.0175	101	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063665.1	s__Limnohabitans_A sp003063665	78.0142	89	185	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.02	95.55	0.82	0.79	4	-
--------------------------------------------------------------------------------
[2023-06-19 01:47:06,327] [INFO] GTDB search result was written to GCA_018005035.1_ASM1800503v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:47:06,328] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:47:06,332] [INFO] DFAST_QC result json was written to GCA_018005035.1_ASM1800503v1_genomic.fna/dqc_result.json
[2023-06-19 01:47:06,332] [INFO] DFAST_QC completed!
[2023-06-19 01:47:06,333] [INFO] Total running time: 0h0m37s