[2024-01-24 12:36:20,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:20,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:20,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference
[2024-01-24 12:36:21,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:21,796] [INFO] Task started: Prodigal
[2024-01-24 12:36:21,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgfba95c9d-f0f6-461a-8879-78effd90f85b/GCF_015461845.1_ASM1546184v1_genomic.fna.gz | prodigal -d GCF_015461845.1_ASM1546184v1_genomic.fna/cds.fna -a GCF_015461845.1_ASM1546184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:44,898] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:44,899] [INFO] Task started: HMMsearch
[2024-01-24 12:36:44,899] [INFO] Running command: hmmsearch --tblout GCF_015461845.1_ASM1546184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference/reference_markers.hmm GCF_015461845.1_ASM1546184v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:45,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:45,255] [INFO] Found 6/6 markers.
[2024-01-24 12:36:45,313] [INFO] Query marker FASTA was written to GCF_015461845.1_ASM1546184v1_genomic.fna/markers.fasta
[2024-01-24 12:36:45,314] [INFO] Task started: Blastn
[2024-01-24 12:36:45,314] [INFO] Running command: blastn -query GCF_015461845.1_ASM1546184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference/reference_markers.fasta -out GCF_015461845.1_ASM1546184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:46,243] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:46,246] [INFO] Selected 14 target genomes.
[2024-01-24 12:36:46,247] [INFO] Target genome list was writen to GCF_015461845.1_ASM1546184v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:46,254] [INFO] Task started: fastANI
[2024-01-24 12:36:46,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba95c9d-f0f6-461a-8879-78effd90f85b/GCF_015461845.1_ASM1546184v1_genomic.fna.gz --refList GCF_015461845.1_ASM1546184v1_genomic.fna/target_genomes.txt --output GCF_015461845.1_ASM1546184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:08,226] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:08,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:08,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:08,245] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:08,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:08,246] [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 mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	88.9471	1834	2338	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	88.9363	1809	2338	95	below_threshold
Pseudomonas mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	88.9137	1843	2338	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	87.7079	1552	2338	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	87.7028	1555	2338	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	87.6864	1556	2338	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	86.7948	1581	2338	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	86.7566	1543	2338	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	86.6621	1563	2338	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	86.5979	1517	2338	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.0483	1492	2338	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.9798	1452	2338	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.5695	1506	2338	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.44	1255	2338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:08,248] [INFO] DFAST Taxonomy check result was written to GCF_015461845.1_ASM1546184v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:08,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:08,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:08,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference/checkm_data
[2024-01-24 12:37:08,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:08,314] [INFO] Task started: CheckM
[2024-01-24 12:37:08,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015461845.1_ASM1546184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015461845.1_ASM1546184v1_genomic.fna/checkm_input GCF_015461845.1_ASM1546184v1_genomic.fna/checkm_result
[2024-01-24 12:38:15,096] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:15,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:15,125] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:15,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:15,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015461845.1_ASM1546184v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:15,126] [INFO] Task started: Blastn
[2024-01-24 12:38:15,126] [INFO] Running command: blastn -query GCF_015461845.1_ASM1546184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb09df81d-a58b-46e5-97a7-bcf66c6e9c18/dqc_reference/reference_markers_gtdb.fasta -out GCF_015461845.1_ASM1546184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:16,740] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:16,743] [INFO] Selected 10 target genomes.
[2024-01-24 12:38:16,743] [INFO] Target genome list was writen to GCF_015461845.1_ASM1546184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:16,754] [INFO] Task started: fastANI
[2024-01-24 12:38:16,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba95c9d-f0f6-461a-8879-78effd90f85b/GCF_015461845.1_ASM1546184v1_genomic.fna.gz --refList GCF_015461845.1_ASM1546184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015461845.1_ASM1546184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:34,434] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:34,446] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:34,447] [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_015461845.1	s__Pseudomonas_E mucoides	100.0	2337	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.43	0.93	0.92	3	conclusive
GCF_003732265.1	s__Pseudomonas_E brassicacearum_D	94.5316	1840	2338	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_006438915.1	s__Pseudomonas_E arsenicoxydans_A	93.8057	1796	2338	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_000282215.1	s__Pseudomonas_E sp000282215	90.3806	1557	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.42	97.42	0.82	0.82	2	-
GCF_002000165.1	s__Pseudomonas_E sp002000165	90.3361	1730	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	98.58	0.93	0.91	3	-
GCF_900106065.1	s__Pseudomonas_E mandelii	88.9137	1843	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.92	98.70	0.92	0.88	64	-
GCF_000968015.1	s__Pseudomonas_E fluorescens_W	88.5666	1622	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_900187425.1	s__Pseudomonas_E sp900187425	88.4863	1661	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.77	95.75	0.84	0.83	4	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	88.1993	1575	2338	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_002091715.1	s__Pseudomonas_E migulae	87.962	1571	2338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.09	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:34,448] [INFO] GTDB search result was written to GCF_015461845.1_ASM1546184v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:34,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:34,452] [INFO] DFAST_QC result json was written to GCF_015461845.1_ASM1546184v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:34,452] [INFO] DFAST_QC completed!
[2024-01-24 12:38:34,452] [INFO] Total running time: 0h2m14s