[2024-01-24 12:06:14,288] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference
[2024-01-24 12:06:15,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,785] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg28802d4a-6030-4a20-951c-ed95f7b739e0/GCF_021601385.1_ASM2160138v1_genomic.fna.gz | prodigal -d GCF_021601385.1_ASM2160138v1_genomic.fna/cds.fna -a GCF_021601385.1_ASM2160138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:36,222] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:36,223] [INFO] Task started: HMMsearch
[2024-01-24 12:06:36,223] [INFO] Running command: hmmsearch --tblout GCF_021601385.1_ASM2160138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference/reference_markers.hmm GCF_021601385.1_ASM2160138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:36,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:36,630] [INFO] Found 6/6 markers.
[2024-01-24 12:06:36,683] [INFO] Query marker FASTA was written to GCF_021601385.1_ASM2160138v1_genomic.fna/markers.fasta
[2024-01-24 12:06:36,684] [INFO] Task started: Blastn
[2024-01-24 12:06:36,684] [INFO] Running command: blastn -query GCF_021601385.1_ASM2160138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference/reference_markers.fasta -out GCF_021601385.1_ASM2160138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:37,743] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:37,746] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:37,747] [INFO] Target genome list was writen to GCF_021601385.1_ASM2160138v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:37,755] [INFO] Task started: fastANI
[2024-01-24 12:06:37,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg28802d4a-6030-4a20-951c-ed95f7b739e0/GCF_021601385.1_ASM2160138v1_genomic.fna.gz --refList GCF_021601385.1_ASM2160138v1_genomic.fna/target_genomes.txt --output GCF_021601385.1_ASM2160138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:08,490] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:08,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:08,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:08,506] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:08,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:08,506] [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 sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	94.0636	1593	1924	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	93.9926	1617	1924	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	89.1568	1410	1924	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	88.9733	1449	1924	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	88.9132	1456	1924	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	88.8866	1464	1924	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	88.8699	1456	1924	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	88.726	1457	1924	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	88.6721	1425	1924	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	88.6496	1426	1924	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	88.6319	1414	1924	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.9384	1373	1924	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.9367	1296	1924	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.8652	1333	1924	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.8352	1316	1924	95	below_threshold
Pseudomonas farsensis	strain=SWRI107	GCA_014268805.2	2745492	2745492	type	True	86.5893	1277	1924	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	86.0469	1287	1924	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	86.0422	1300	1924	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	80.9467	792	1924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:08,507] [INFO] DFAST Taxonomy check result was written to GCF_021601385.1_ASM2160138v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:08,508] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:08,508] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:08,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference/checkm_data
[2024-01-24 12:07:08,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:08,566] [INFO] Task started: CheckM
[2024-01-24 12:07:08,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021601385.1_ASM2160138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021601385.1_ASM2160138v1_genomic.fna/checkm_input GCF_021601385.1_ASM2160138v1_genomic.fna/checkm_result
[2024-01-24 12:08:08,375] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:08,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:08,403] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:08,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:08,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021601385.1_ASM2160138v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:08,404] [INFO] Task started: Blastn
[2024-01-24 12:08:08,404] [INFO] Running command: blastn -query GCF_021601385.1_ASM2160138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10afa8c4-a31e-4e73-9ecc-79922dd0eeb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_021601385.1_ASM2160138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:10,283] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:10,288] [INFO] Selected 17 target genomes.
[2024-01-24 12:08:10,288] [INFO] Target genome list was writen to GCF_021601385.1_ASM2160138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:10,305] [INFO] Task started: fastANI
[2024-01-24 12:08:10,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg28802d4a-6030-4a20-951c-ed95f7b739e0/GCF_021601385.1_ASM2160138v1_genomic.fna.gz --refList GCF_021601385.1_ASM2160138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021601385.1_ASM2160138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:37,439] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:37,457] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:08:37,458] [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_003231305.1	s__Pseudomonas_E sichuanensis	94.065	1593	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_015354575.1	s__Pseudomonas_E sp015354575	90.4472	1520	1924	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_003205295.1	s__Pseudomonas_E mosselii_B	89.2005	1438	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_016861355.1	s__Pseudomonas_E sp001259595	89.1839	1474	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	89.1656	1409	1924	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_000621225.1	s__Pseudomonas_E mosselii	88.9039	1456	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_018417595.1	s__Pseudomonas_E entomophila_C	88.9008	1482	1924	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_000026105.1	s__Pseudomonas_E entomophila	88.8874	1465	1924	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_019139675.1	s__Pseudomonas_E sp019139675	88.8406	1459	1924	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	88.751	1367	1924	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_014268885.2	s__Pseudomonas_E sp014268885	88.6576	1426	1924	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_900110655.1	s__Pseudomonas_E soli	88.6454	1427	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCF_011752525.1	s__Pseudomonas_E sp011752525	88.4259	1375	1924	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_013373935.1	s__Pseudomonas_E sp002438125	87.9573	1294	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_003097235.1	s__Pseudomonas_E sp003097235	87.4937	1352	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	87.4846	1376	1924	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_000282535.1	s__Pseudomonas_E sp000282535	87.1192	1214	1924	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:37,459] [INFO] GTDB search result was written to GCF_021601385.1_ASM2160138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:37,460] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:37,464] [INFO] DFAST_QC result json was written to GCF_021601385.1_ASM2160138v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:37,464] [INFO] DFAST_QC completed!
[2024-01-24 12:08:37,464] [INFO] Total running time: 0h2m23s