[2024-01-24 14:05:48,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:48,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:48,728] [INFO] DQC Reference Directory: /var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference
[2024-01-24 14:05:50,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,051] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,051] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf88173c-ca29-42fb-93a0-0604b3ecaa78/GCF_022548835.1_ASM2254883v1_genomic.fna.gz | prodigal -d GCF_022548835.1_ASM2254883v1_genomic.fna/cds.fna -a GCF_022548835.1_ASM2254883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:09,990] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:09,990] [INFO] Task started: HMMsearch
[2024-01-24 14:06:09,990] [INFO] Running command: hmmsearch --tblout GCF_022548835.1_ASM2254883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference/reference_markers.hmm GCF_022548835.1_ASM2254883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:10,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:10,305] [INFO] Found 6/6 markers.
[2024-01-24 14:06:10,360] [INFO] Query marker FASTA was written to GCF_022548835.1_ASM2254883v1_genomic.fna/markers.fasta
[2024-01-24 14:06:10,360] [INFO] Task started: Blastn
[2024-01-24 14:06:10,360] [INFO] Running command: blastn -query GCF_022548835.1_ASM2254883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference/reference_markers.fasta -out GCF_022548835.1_ASM2254883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:11,493] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:11,496] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:11,497] [INFO] Target genome list was writen to GCF_022548835.1_ASM2254883v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:11,503] [INFO] Task started: fastANI
[2024-01-24 14:06:11,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf88173c-ca29-42fb-93a0-0604b3ecaa78/GCF_022548835.1_ASM2254883v1_genomic.fna.gz --refList GCF_022548835.1_ASM2254883v1_genomic.fna/target_genomes.txt --output GCF_022548835.1_ASM2254883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:32,467] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:32,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:32,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:32,481] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:32,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:32,482] [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 capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	100.0	1746	1767	95	conclusive
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	99.9785	1763	1767	95	conclusive
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	90.7947	1520	1767	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.9468	1304	1767	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.9448	1241	1767	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	87.8525	1404	1767	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	87.8129	1394	1767	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	87.7537	1436	1767	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.8822	1296	1767	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	86.8122	1267	1767	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	86.8084	1284	1767	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.7978	1270	1767	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	86.5497	1221	1767	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	86.4766	1243	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,484] [INFO] DFAST Taxonomy check result was written to GCF_022548835.1_ASM2254883v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:32,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:32,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:32,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference/checkm_data
[2024-01-24 14:06:32,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:32,559] [INFO] Task started: CheckM
[2024-01-24 14:06:32,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022548835.1_ASM2254883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022548835.1_ASM2254883v1_genomic.fna/checkm_input GCF_022548835.1_ASM2254883v1_genomic.fna/checkm_result
[2024-01-24 14:07:29,092] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:29,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:29,111] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:29,111] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:29,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022548835.1_ASM2254883v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:29,112] [INFO] Task started: Blastn
[2024-01-24 14:07:29,113] [INFO] Running command: blastn -query GCF_022548835.1_ASM2254883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee576af4-b3c4-4587-bf9a-4c1cd9229a82/dqc_reference/reference_markers_gtdb.fasta -out GCF_022548835.1_ASM2254883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:31,065] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:31,069] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:31,069] [INFO] Target genome list was writen to GCF_022548835.1_ASM2254883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:31,086] [INFO] Task started: fastANI
[2024-01-24 14:07:31,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf88173c-ca29-42fb-93a0-0604b3ecaa78/GCF_022548835.1_ASM2254883v1_genomic.fna.gz --refList GCF_022548835.1_ASM2254883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022548835.1_ASM2254883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:59,332] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:59,351] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:59,351] [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_000731675.1	s__Pseudomonas_E capeferrum	99.9785	1763	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	conclusive
GCF_002736125.1	s__Pseudomonas_E putida_M	90.8183	1530	1767	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_000935045.1	s__Pseudomonas_E sp000935045	88.3503	1309	1767	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_001642705.1	s__Pseudomonas_E sp001642705	88.2351	1362	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_013373935.1	s__Pseudomonas_E sp002438125	87.9813	1238	1767	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_000708715.2	s__Pseudomonas_E putida_R	87.9127	1452	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.68	95.68	0.85	0.85	2	-
GCF_000412675.1	s__Pseudomonas_E putida	87.7761	1426	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	87.7434	1344	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	87.6817	1287	1767	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_000498395.2	s__Pseudomonas_E putida_Q	87.6634	1465	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	97.78	0.93	0.90	5	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	87.511	1201	1767	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_003097235.1	s__Pseudomonas_E sp003097235	87.4444	1332	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	87.4316	1232	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_009883635.2	s__Pseudomonas_E putida_W	87.3749	1332	1767	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	87.3368	1239	1767	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_002356095.1	s__Pseudomonas_E putida_H	87.2484	1445	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.82	98.35	0.91	0.82	20	-
GCF_001320245.1	s__Pseudomonas_E sp001320245	86.9936	1271	1767	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_000019445.1	s__Pseudomonas_E putida_E	86.6974	1285	1767	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	86.5554	1220	1767	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	86.2293	1187	1767	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 14:07:59,354] [INFO] GTDB search result was written to GCF_022548835.1_ASM2254883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:59,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:59,361] [INFO] DFAST_QC result json was written to GCF_022548835.1_ASM2254883v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:59,361] [INFO] DFAST_QC completed!
[2024-01-24 14:07:59,361] [INFO] Total running time: 0h2m11s