[2024-01-25 18:53:21,044] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:21,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:21,051] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference
[2024-01-25 18:53:22,204] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:22,205] [INFO] Task started: Prodigal
[2024-01-25 18:53:22,205] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a71ee50-8a98-48b9-88c3-f9b447de65c5/GCF_012034345.1_ASM1203434v1_genomic.fna.gz | prodigal -d GCF_012034345.1_ASM1203434v1_genomic.fna/cds.fna -a GCF_012034345.1_ASM1203434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:45,286] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:45,286] [INFO] Task started: HMMsearch
[2024-01-25 18:53:45,286] [INFO] Running command: hmmsearch --tblout GCF_012034345.1_ASM1203434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference/reference_markers.hmm GCF_012034345.1_ASM1203434v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:45,567] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:45,568] [INFO] Found 6/6 markers.
[2024-01-25 18:53:45,619] [INFO] Query marker FASTA was written to GCF_012034345.1_ASM1203434v1_genomic.fna/markers.fasta
[2024-01-25 18:53:45,619] [INFO] Task started: Blastn
[2024-01-25 18:53:45,619] [INFO] Running command: blastn -query GCF_012034345.1_ASM1203434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference/reference_markers.fasta -out GCF_012034345.1_ASM1203434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:46,513] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:46,516] [INFO] Selected 11 target genomes.
[2024-01-25 18:53:46,516] [INFO] Target genome list was writen to GCF_012034345.1_ASM1203434v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:46,532] [INFO] Task started: fastANI
[2024-01-25 18:53:46,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a71ee50-8a98-48b9-88c3-f9b447de65c5/GCF_012034345.1_ASM1203434v1_genomic.fna.gz --refList GCF_012034345.1_ASM1203434v1_genomic.fna/target_genomes.txt --output GCF_012034345.1_ASM1203434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:09,304] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:09,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:09,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:09,314] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:54:09,314] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:09,314] [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 brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	100.0	2217	2219	95	conclusive
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	99.9966	2210	2219	95	conclusive
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	94.9309	1839	2219	95	below_threshold
Pseudomonas bijieensis	strain=L22-9	GCA_013347965.1	2681983	2681983	type	True	92.2994	1898	2219	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	92.2355	1873	2219	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	91.7782	1736	2219	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	88.7017	1684	2219	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	84.5961	1353	2219	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	84.5833	1321	2219	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	83.7755	1320	2219	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.4332	1220	2219	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:09,315] [INFO] DFAST Taxonomy check result was written to GCF_012034345.1_ASM1203434v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:09,316] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:09,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:09,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference/checkm_data
[2024-01-25 18:54:09,317] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:09,381] [INFO] Task started: CheckM
[2024-01-25 18:54:09,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034345.1_ASM1203434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034345.1_ASM1203434v1_genomic.fna/checkm_input GCF_012034345.1_ASM1203434v1_genomic.fna/checkm_result
[2024-01-25 18:55:13,844] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:13,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:13,870] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:13,870] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:13,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034345.1_ASM1203434v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:13,871] [INFO] Task started: Blastn
[2024-01-25 18:55:13,871] [INFO] Running command: blastn -query GCF_012034345.1_ASM1203434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe609491-c3a2-4238-8116-f2b2a3f78a25/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034345.1_ASM1203434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:15,542] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:15,545] [INFO] Selected 8 target genomes.
[2024-01-25 18:55:15,545] [INFO] Target genome list was writen to GCF_012034345.1_ASM1203434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:15,549] [INFO] Task started: fastANI
[2024-01-25 18:55:15,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a71ee50-8a98-48b9-88c3-f9b447de65c5/GCF_012034345.1_ASM1203434v1_genomic.fna.gz --refList GCF_012034345.1_ASM1203434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034345.1_ASM1203434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:36,426] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:36,432] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:36,432] [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_008801605.1	s__Pseudomonas_E brassicacearum	99.9966	2210	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	96.48	0.95	0.86	21	conclusive
GCF_001269885.1	s__Pseudomonas_E kilonensis	94.9355	1838	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.12	95.91	0.90	0.87	15	-
GCF_009601685.2	s__Pseudomonas_E kilonensis_B	94.4547	1875	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.30	99.26	0.94	0.93	4	-
GCF_001623525.1	s__Pseudomonas_E fluorescens_Q	94.353	1858	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.03	97.11	0.90	0.89	14	-
GCF_018325905.1	s__Pseudomonas_E sp018325905	93.8864	1855	2219	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_900581005.1	s__Pseudomonas_E sp900581005	92.4756	1811	2219	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_001307275.1	s__Pseudomonas_E fluorescens_AA	92.372	1883	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.99	95.90	0.90	0.85	18	-
GCF_001269655.1	s__Pseudomonas_E thivervalensis	92.2254	1874	2219	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:36,435] [INFO] GTDB search result was written to GCF_012034345.1_ASM1203434v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:36,436] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:36,440] [INFO] DFAST_QC result json was written to GCF_012034345.1_ASM1203434v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:36,440] [INFO] DFAST_QC completed!
[2024-01-25 18:55:36,440] [INFO] Total running time: 0h2m15s