[2024-01-24 13:13:39,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,252] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference
[2024-01-24 13:13:40,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,473] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,473] [INFO] Running command: gunzip -c /var/lib/cwl/stgce00b8b7-8fd2-46dd-a4fc-117cdfe9bab4/GCF_003231305.1_ASM323130v1_genomic.fna.gz | prodigal -d GCF_003231305.1_ASM323130v1_genomic.fna/cds.fna -a GCF_003231305.1_ASM323130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:00,894] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:00,894] [INFO] Task started: HMMsearch
[2024-01-24 13:14:00,894] [INFO] Running command: hmmsearch --tblout GCF_003231305.1_ASM323130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference/reference_markers.hmm GCF_003231305.1_ASM323130v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:01,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:01,180] [INFO] Found 6/6 markers.
[2024-01-24 13:14:01,229] [INFO] Query marker FASTA was written to GCF_003231305.1_ASM323130v1_genomic.fna/markers.fasta
[2024-01-24 13:14:01,229] [INFO] Task started: Blastn
[2024-01-24 13:14:01,229] [INFO] Running command: blastn -query GCF_003231305.1_ASM323130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference/reference_markers.fasta -out GCF_003231305.1_ASM323130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:02,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:02,201] [INFO] Selected 19 target genomes.
[2024-01-24 13:14:02,202] [INFO] Target genome list was writen to GCF_003231305.1_ASM323130v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:02,211] [INFO] Task started: fastANI
[2024-01-24 13:14:02,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgce00b8b7-8fd2-46dd-a4fc-117cdfe9bab4/GCF_003231305.1_ASM323130v1_genomic.fna.gz --refList GCF_003231305.1_ASM323130v1_genomic.fna/target_genomes.txt --output GCF_003231305.1_ASM323130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:27,895] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:27,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:27,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:27,910] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:27,910] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:14:27,910] [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	100.0	1928	1937	95	inconclusive
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	96.2393	1674	1937	95	inconclusive
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	89.0981	1376	1937	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	89.0562	1405	1937	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	88.9816	1414	1937	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	88.9433	1451	1937	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	88.9133	1403	1937	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	88.7163	1386	1937	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	88.6939	1414	1937	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.7904	1346	1937	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.771	1286	1937	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.8106	1337	1937	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.7163	1306	1937	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.6366	1232	1937	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	86.044	1273	1937	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	86.028	1279	1937	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.4341	844	1937	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	75.9183	165	1937	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	75.5365	75	1937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:27,912] [INFO] DFAST Taxonomy check result was written to GCF_003231305.1_ASM323130v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:27,913] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:27,913] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:27,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference/checkm_data
[2024-01-24 13:14:27,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:27,968] [INFO] Task started: CheckM
[2024-01-24 13:14:27,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003231305.1_ASM323130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003231305.1_ASM323130v1_genomic.fna/checkm_input GCF_003231305.1_ASM323130v1_genomic.fna/checkm_result
[2024-01-24 13:15:24,520] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:24,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:24,540] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:24,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:24,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003231305.1_ASM323130v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:24,541] [INFO] Task started: Blastn
[2024-01-24 13:15:24,542] [INFO] Running command: blastn -query GCF_003231305.1_ASM323130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1154bf7-f948-48c4-a75e-10129b549c23/dqc_reference/reference_markers_gtdb.fasta -out GCF_003231305.1_ASM323130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:26,089] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:26,092] [INFO] Selected 15 target genomes.
[2024-01-24 13:15:26,092] [INFO] Target genome list was writen to GCF_003231305.1_ASM323130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:26,114] [INFO] Task started: fastANI
[2024-01-24 13:15:26,114] [INFO] Running command: fastANI --query /var/lib/cwl/stgce00b8b7-8fd2-46dd-a4fc-117cdfe9bab4/GCF_003231305.1_ASM323130v1_genomic.fna.gz --refList GCF_003231305.1_ASM323130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003231305.1_ASM323130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:49,150] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:49,165] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:49,166] [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	100.0	1928	1937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	conclusive
GCF_015354575.1	s__Pseudomonas_E sp015354575	90.2601	1517	1937	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_016861355.1	s__Pseudomonas_E sp001259595	89.2738	1420	1937	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_003205295.1	s__Pseudomonas_E mosselii_B	89.1621	1403	1937	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_019139535.1	s__Pseudomonas_E sp019139535	89.1181	1373	1937	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	89.045	1407	1937	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_000026105.1	s__Pseudomonas_E entomophila	88.9497	1450	1937	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_018417595.1	s__Pseudomonas_E entomophila_C	88.8373	1464	1937	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	88.7205	1411	1937	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_004519305.1	s__Pseudomonas_E sp004519305	88.6774	1360	1937	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_011752525.1	s__Pseudomonas_E sp011752525	88.3447	1335	1937	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	87.7128	1293	1937	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_000282535.1	s__Pseudomonas_E sp000282535	87.016	1213	1937	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_013523055.1	s__Pseudomonas_E capeferrum_A	83.3996	1089	1937	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_000931465.1	s__Pseudomonas_E sp000931465	82.9501	1167	1937	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:49,167] [INFO] GTDB search result was written to GCF_003231305.1_ASM323130v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:49,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:49,172] [INFO] DFAST_QC result json was written to GCF_003231305.1_ASM323130v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:49,172] [INFO] DFAST_QC completed!
[2024-01-24 13:15:49,172] [INFO] Total running time: 0h2m10s