[2024-01-24 13:22:10,781] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,783] [INFO] DQC Reference Directory: /var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference
[2024-01-24 13:22:12,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:12,117] [INFO] Task started: Prodigal
[2024-01-24 13:22:12,117] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6547a80-6d15-4f62-9f45-7b0606703305/GCF_012033695.1_ASM1203369v1_genomic.fna.gz | prodigal -d GCF_012033695.1_ASM1203369v1_genomic.fna/cds.fna -a GCF_012033695.1_ASM1203369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:30,422] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:30,423] [INFO] Task started: HMMsearch
[2024-01-24 13:22:30,423] [INFO] Running command: hmmsearch --tblout GCF_012033695.1_ASM1203369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference/reference_markers.hmm GCF_012033695.1_ASM1203369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:30,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:30,764] [INFO] Found 6/6 markers.
[2024-01-24 13:22:30,812] [INFO] Query marker FASTA was written to GCF_012033695.1_ASM1203369v1_genomic.fna/markers.fasta
[2024-01-24 13:22:30,813] [INFO] Task started: Blastn
[2024-01-24 13:22:30,813] [INFO] Running command: blastn -query GCF_012033695.1_ASM1203369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference/reference_markers.fasta -out GCF_012033695.1_ASM1203369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:31,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:31,864] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:31,865] [INFO] Target genome list was writen to GCF_012033695.1_ASM1203369v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:31,877] [INFO] Task started: fastANI
[2024-01-24 13:22:31,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6547a80-6d15-4f62-9f45-7b0606703305/GCF_012033695.1_ASM1203369v1_genomic.fna.gz --refList GCF_012033695.1_ASM1203369v1_genomic.fna/target_genomes.txt --output GCF_012033695.1_ASM1203369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:50,803] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:50,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:50,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:50,819] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:50,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:50,819] [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
Pseudomonas quercus	strain=hsmgli-8	GCA_012033695.1	2722792	2722792	type	True	100.0	1634	1639	95	conclusive
Pseudomonas massiliensis	strain=CB1	GCA_000826105.1	522492	522492	type	True	80.7274	799	1639	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	79.5817	642	1639	95	below_threshold
Pseudomonas coleopterorum	strain=LMG 28558	GCA_900105555.1	1605838	1605838	type	True	79.1711	596	1639	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	79.1657	576	1639	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	79.1612	491	1639	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	79.1556	545	1639	95	below_threshold
Pseudomonas rhizosphaerae	strain=DSM 16299	GCA_000761155.1	216142	216142	type	True	79.1409	584	1639	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	79.1137	552	1639	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	79.1133	545	1639	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	79.0796	553	1639	95	below_threshold
Pseudomonas baltica	strain=MBT-2	GCA_014235765.1	2762576	2762576	type	True	79.0715	582	1639	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	79.0711	554	1639	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	79.0148	552	1639	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	79.0131	526	1639	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	78.9603	565	1639	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	78.9004	531	1639	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	78.6222	392	1639	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	78.3802	421	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:50,821] [INFO] DFAST Taxonomy check result was written to GCF_012033695.1_ASM1203369v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:50,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:50,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:50,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference/checkm_data
[2024-01-24 13:22:50,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:50,869] [INFO] Task started: CheckM
[2024-01-24 13:22:50,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012033695.1_ASM1203369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012033695.1_ASM1203369v1_genomic.fna/checkm_input GCF_012033695.1_ASM1203369v1_genomic.fna/checkm_result
[2024-01-24 13:23:42,869] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:42,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:42,903] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:42,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:42,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012033695.1_ASM1203369v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:42,904] [INFO] Task started: Blastn
[2024-01-24 13:23:42,905] [INFO] Running command: blastn -query GCF_012033695.1_ASM1203369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb95b4a95-d095-4c21-b210-61c843bd7efb/dqc_reference/reference_markers_gtdb.fasta -out GCF_012033695.1_ASM1203369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:44,500] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:44,505] [INFO] Selected 15 target genomes.
[2024-01-24 13:23:44,505] [INFO] Target genome list was writen to GCF_012033695.1_ASM1203369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:44,563] [INFO] Task started: fastANI
[2024-01-24 13:23:44,564] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6547a80-6d15-4f62-9f45-7b0606703305/GCF_012033695.1_ASM1203369v1_genomic.fna.gz --refList GCF_012033695.1_ASM1203369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012033695.1_ASM1203369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:00,310] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:00,322] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:00,323] [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_012033695.1	s__Pseudomonas_E quercus	100.0	1636	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013522925.1	s__Pseudomonas_E japonica_A	81.423	931	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.09	99.09	0.96	0.96	2	-
GCF_000826105.1	s__Pseudomonas_E massiliensis	80.7182	800	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013374995.1	s__Pseudomonas_E eucalypticola	79.5534	645	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	99.03	0.96	0.96	2	-
GCF_002806685.1	s__Pseudomonas_E qingdaonensis	79.4476	577	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.05	98.91	0.93	0.89	13	-
GCA_000497835.1	s__Pseudomonas_E sp000497835	79.4376	666	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434265.1	s__Pseudomonas_E sp002434265	79.1828	523	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105555.1	s__Pseudomonas_E coleopterorum	79.1793	596	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.66	96.53	0.90	0.88	9	-
GCF_000761155.1	s__Pseudomonas_E rhizosphaerae	79.1659	580	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.13	98.13	0.92	0.92	2	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	79.157	567	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097135.1	s__Pseudomonas_E sp003097135	79.1532	534	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	4	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	79.1422	539	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	79.1252	541	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293465.1	s__Pseudomonas_E fuscovaginae_B	78.9887	599	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.24	0.95	0.95	2	-
GCF_900589395.1	s__Pseudomonas_E sp900589395	78.8693	567	1639	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.24	99.16	0.94	0.93	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,325] [INFO] GTDB search result was written to GCF_012033695.1_ASM1203369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:00,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:00,329] [INFO] DFAST_QC result json was written to GCF_012033695.1_ASM1203369v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:00,330] [INFO] DFAST_QC completed!
[2024-01-24 13:24:00,330] [INFO] Total running time: 0h1m50s