[2024-01-24 11:59:51,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,988] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference
[2024-01-24 11:59:55,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,383] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg56b3e824-bd62-4f17-8fc7-aadf4dd68809/GCF_014268815.2_ASM1426881v2_genomic.fna.gz | prodigal -d GCF_014268815.2_ASM1426881v2_genomic.fna/cds.fna -a GCF_014268815.2_ASM1426881v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:16,183] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:16,183] [INFO] Task started: HMMsearch
[2024-01-24 12:00:16,183] [INFO] Running command: hmmsearch --tblout GCF_014268815.2_ASM1426881v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference/reference_markers.hmm GCF_014268815.2_ASM1426881v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:16,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:16,482] [INFO] Found 6/6 markers.
[2024-01-24 12:00:16,533] [INFO] Query marker FASTA was written to GCF_014268815.2_ASM1426881v2_genomic.fna/markers.fasta
[2024-01-24 12:00:16,533] [INFO] Task started: Blastn
[2024-01-24 12:00:16,533] [INFO] Running command: blastn -query GCF_014268815.2_ASM1426881v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference/reference_markers.fasta -out GCF_014268815.2_ASM1426881v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:17,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:17,575] [INFO] Selected 22 target genomes.
[2024-01-24 12:00:17,576] [INFO] Target genome list was writen to GCF_014268815.2_ASM1426881v2_genomic.fna/target_genomes.txt
[2024-01-24 12:00:17,589] [INFO] Task started: fastANI
[2024-01-24 12:00:17,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b3e824-bd62-4f17-8fc7-aadf4dd68809/GCF_014268815.2_ASM1426881v2_genomic.fna.gz --refList GCF_014268815.2_ASM1426881v2_genomic.fna/target_genomes.txt --output GCF_014268815.2_ASM1426881v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:46,624] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:46,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:46,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:46,642] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:46,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:46,642] [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 faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	86.3858	1273	1926	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	86.2861	1358	1926	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	86.0077	1333	1926	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	85.9499	1365	1926	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	85.7431	1361	1926	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	85.6894	1392	1926	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	85.6756	1355	1926	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	85.619	1224	1926	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	85.6141	1255	1926	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	85.6119	1382	1926	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	85.6088	1260	1926	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	85.6063	1359	1926	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	85.5629	1334	1926	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	85.5083	1325	1926	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	85.438	1291	1926	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	85.4212	1367	1926	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	85.3527	1331	1926	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	85.3521	1335	1926	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	85.3402	1352	1926	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	85.2791	1316	1926	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	84.9433	1267	1926	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	84.9312	1283	1926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:46,644] [INFO] DFAST Taxonomy check result was written to GCF_014268815.2_ASM1426881v2_genomic.fna/tc_result.tsv
[2024-01-24 12:00:46,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:46,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:46,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference/checkm_data
[2024-01-24 12:00:46,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:46,699] [INFO] Task started: CheckM
[2024-01-24 12:00:46,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268815.2_ASM1426881v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268815.2_ASM1426881v2_genomic.fna/checkm_input GCF_014268815.2_ASM1426881v2_genomic.fna/checkm_result
[2024-01-24 12:01:45,283] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:45,285] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:45,309] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:45,309] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:45,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268815.2_ASM1426881v2_genomic.fna/markers.fasta)
[2024-01-24 12:01:45,310] [INFO] Task started: Blastn
[2024-01-24 12:01:45,310] [INFO] Running command: blastn -query GCF_014268815.2_ASM1426881v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6f5df23-5912-459f-83d8-429c9cdd7983/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268815.2_ASM1426881v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:47,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:47,191] [INFO] Selected 16 target genomes.
[2024-01-24 12:01:47,191] [INFO] Target genome list was writen to GCF_014268815.2_ASM1426881v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:47,205] [INFO] Task started: fastANI
[2024-01-24 12:01:47,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b3e824-bd62-4f17-8fc7-aadf4dd68809/GCF_014268815.2_ASM1426881v2_genomic.fna.gz --refList GCF_014268815.2_ASM1426881v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268815.2_ASM1426881v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:09,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:09,881] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:09,882] [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_014268815.2	s__Pseudomonas_E sp014268815	100.0	1926	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900536025.1	s__Pseudomonas_E reidholzensis	87.6837	1416	1926	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_017875955.1	s__Pseudomonas_E sp017875955	86.9408	1370	1926	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	86.3866	1273	1926	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_003231305.1	s__Pseudomonas_E sichuanensis	86.0078	1333	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	85.9485	1294	1926	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_019139535.1	s__Pseudomonas_E sp019139535	85.9375	1366	1926	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	85.9254	1188	1926	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_000730665.1	s__Pseudomonas_E plecoglossicida	85.6207	1258	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	-
GCF_000731675.1	s__Pseudomonas_E capeferrum	85.5919	1361	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	85.5712	1320	1926	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_002736125.1	s__Pseudomonas_E putida_M	85.5495	1348	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
GCF_002843585.1	s__Pseudomonas_E sp002843585	85.531	1326	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	97.16	0.92	0.88	9	-
GCF_005080685.1	s__Pseudomonas_E putida_V	85.1968	1373	1926	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_003627215.1	s__Pseudomonas_E sp001422615	84.93	1315	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001320525.1	s__Pseudomonas_E sp001320525	84.9157	1287	1926	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	98.78	0.89	0.86	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:09,884] [INFO] GTDB search result was written to GCF_014268815.2_ASM1426881v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:09,884] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:09,889] [INFO] DFAST_QC result json was written to GCF_014268815.2_ASM1426881v2_genomic.fna/dqc_result.json
[2024-01-24 12:02:09,889] [INFO] DFAST_QC completed!
[2024-01-24 12:02:09,890] [INFO] Total running time: 0h2m18s