[2024-01-24 11:35:34,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference
[2024-01-24 11:35:35,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,821] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d799cd5-9880-4a36-af9a-1cbd227d469b/GCF_003586265.1_ASM358626v1_genomic.fna.gz | prodigal -d GCF_003586265.1_ASM358626v1_genomic.fna/cds.fna -a GCF_003586265.1_ASM358626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:47,640] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:47,640] [INFO] Task started: HMMsearch
[2024-01-24 11:35:47,640] [INFO] Running command: hmmsearch --tblout GCF_003586265.1_ASM358626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference/reference_markers.hmm GCF_003586265.1_ASM358626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:47,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:47,903] [INFO] Found 6/6 markers.
[2024-01-24 11:35:47,935] [INFO] Query marker FASTA was written to GCF_003586265.1_ASM358626v1_genomic.fna/markers.fasta
[2024-01-24 11:35:47,935] [INFO] Task started: Blastn
[2024-01-24 11:35:47,935] [INFO] Running command: blastn -query GCF_003586265.1_ASM358626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference/reference_markers.fasta -out GCF_003586265.1_ASM358626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:48,806] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:48,810] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:48,811] [INFO] Target genome list was writen to GCF_003586265.1_ASM358626v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:48,821] [INFO] Task started: fastANI
[2024-01-24 11:35:48,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d799cd5-9880-4a36-af9a-1cbd227d469b/GCF_003586265.1_ASM358626v1_genomic.fna.gz --refList GCF_003586265.1_ASM358626v1_genomic.fna/target_genomes.txt --output GCF_003586265.1_ASM358626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:08,033] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:08,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:08,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:08,056] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:08,056] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:08,057] [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 yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	80.235	525	1305	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.9539	531	1305	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	79.9465	548	1305	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	79.7781	549	1305	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	79.7419	547	1305	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.6193	476	1305	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.5718	484	1305	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	79.3235	459	1305	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.0881	445	1305	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.9176	434	1305	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.6541	393	1305	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.6335	368	1305	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	78.5587	329	1305	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.5048	387	1305	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	78.3807	355	1305	95	below_threshold
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	78.3746	395	1305	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	78.3568	394	1305	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	78.3568	394	1305	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	78.3164	353	1305	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	78.2789	403	1305	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	78.239	320	1305	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	78.211	334	1305	95	below_threshold
Klebsiella variicola	strain=DSM 15968	GCA_000828055.2	244366	244366	type	True	75.8534	62	1305	95	below_threshold
Klebsiella variicola subsp. variicola	strain=F2R9T	GCA_020525545.1	2590157	244366	type	True	75.8534	62	1305	95	below_threshold
Klebsiella variicola	strain=F2R9	GCA_017638945.1	244366	244366	type	True	75.8534	62	1305	95	below_threshold
Klebsiella variicola	strain=type strain: F2R9	GCA_900978195.1	244366	244366	type	True	75.568	60	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:08,058] [INFO] DFAST Taxonomy check result was written to GCF_003586265.1_ASM358626v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:08,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:08,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:08,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference/checkm_data
[2024-01-24 11:36:08,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:08,097] [INFO] Task started: CheckM
[2024-01-24 11:36:08,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003586265.1_ASM358626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003586265.1_ASM358626v1_genomic.fna/checkm_input GCF_003586265.1_ASM358626v1_genomic.fna/checkm_result
[2024-01-24 11:36:45,362] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:45,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:45,380] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:45,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:45,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003586265.1_ASM358626v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:45,381] [INFO] Task started: Blastn
[2024-01-24 11:36:45,382] [INFO] Running command: blastn -query GCF_003586265.1_ASM358626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6b853c2-27a8-472d-b729-8ca11984ccd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003586265.1_ASM358626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:46,689] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:46,694] [INFO] Selected 20 target genomes.
[2024-01-24 11:36:46,694] [INFO] Target genome list was writen to GCF_003586265.1_ASM358626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:46,729] [INFO] Task started: fastANI
[2024-01-24 11:36:46,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d799cd5-9880-4a36-af9a-1cbd227d469b/GCF_003586265.1_ASM358626v1_genomic.fna.gz --refList GCF_003586265.1_ASM358626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003586265.1_ASM358626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:04,603] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:04,619] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:04,619] [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_003586265.1	s__Pseudomonas_D jilinensis	100.0	1303	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.07	95.47	0.89	0.88	3	conclusive
GCF_900114825.1	s__Pseudomonas_D yangmingensis	80.2052	527	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	80.1014	573	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114765.1	s__Pseudomonas_D pachastrellae	79.9506	548	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	79.8638	550	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	79.8241	512	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	79.7994	479	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	79.7565	545	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	79.6192	476	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	79.5114	398	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646575.1	s__Pseudomonas_D pertucinogena	79.2854	445	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	79.0984	372	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_900105005.1	s__Pseudomonas_D litoralis	79.0896	448	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	79.0698	435	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105655.1	s__Pseudomonas_D salegens	79.0648	451	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	79.018	497	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	78.9505	394	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	78.3837	353	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	78.3108	355	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_000802155.2	s__Pseudomonas_E frederiksbergensis_A	77.7488	299	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.21	99.12	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:04,621] [INFO] GTDB search result was written to GCF_003586265.1_ASM358626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:04,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:04,627] [INFO] DFAST_QC result json was written to GCF_003586265.1_ASM358626v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:04,627] [INFO] DFAST_QC completed!
[2024-01-24 11:37:04,627] [INFO] Total running time: 0h1m30s