[2024-01-24 12:21:44,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,732] [INFO] DQC Reference Directory: /var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference
[2024-01-24 12:21:46,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,172] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg183a40c1-4fee-46a9-98dc-a722507d658e/GCF_008641105.1_ASM864110v1_genomic.fna.gz | prodigal -d GCF_008641105.1_ASM864110v1_genomic.fna/cds.fna -a GCF_008641105.1_ASM864110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:59,503] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:59,504] [INFO] Task started: HMMsearch
[2024-01-24 12:21:59,504] [INFO] Running command: hmmsearch --tblout GCF_008641105.1_ASM864110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference/reference_markers.hmm GCF_008641105.1_ASM864110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:59,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:59,889] [INFO] Found 6/6 markers.
[2024-01-24 12:21:59,932] [INFO] Query marker FASTA was written to GCF_008641105.1_ASM864110v1_genomic.fna/markers.fasta
[2024-01-24 12:21:59,932] [INFO] Task started: Blastn
[2024-01-24 12:21:59,933] [INFO] Running command: blastn -query GCF_008641105.1_ASM864110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference/reference_markers.fasta -out GCF_008641105.1_ASM864110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:00,936] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:00,939] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:00,940] [INFO] Target genome list was writen to GCF_008641105.1_ASM864110v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:00,946] [INFO] Task started: fastANI
[2024-01-24 12:22:00,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg183a40c1-4fee-46a9-98dc-a722507d658e/GCF_008641105.1_ASM864110v1_genomic.fna.gz --refList GCF_008641105.1_ASM864110v1_genomic.fna/target_genomes.txt --output GCF_008641105.1_ASM864110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:16,283] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:16,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:16,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:16,301] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:16,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:16,301] [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
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	100.0	1331	1399	95	conclusive
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	99.9956	1256	1399	95	conclusive
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.6574	325	1399	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.5714	381	1399	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.5328	373	1399	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	78.4842	405	1399	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	78.4649	407	1399	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.461	361	1399	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	78.2291	416	1399	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	78.2069	413	1399	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.8797	266	1399	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	77.6609	219	1399	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	77.5968	216	1399	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	77.4236	239	1399	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.3518	230	1399	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	77.3356	228	1399	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	77.266	233	1399	95	below_threshold
Pseudomonas versuta	strain=L10.10	GCA_001294575.1	1788301	1788301	type	True	77.2221	136	1399	95	below_threshold
Pseudomonas paraversuta	strain=V4/DAB/S4/2a	GCA_904063065.1	2750624	2750624	type	True	77.1034	144	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:16,303] [INFO] DFAST Taxonomy check result was written to GCF_008641105.1_ASM864110v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:16,304] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:16,304] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:16,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference/checkm_data
[2024-01-24 12:22:16,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:16,356] [INFO] Task started: CheckM
[2024-01-24 12:22:16,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008641105.1_ASM864110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008641105.1_ASM864110v1_genomic.fna/checkm_input GCF_008641105.1_ASM864110v1_genomic.fna/checkm_result
[2024-01-24 12:23:01,553] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:01,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:01,600] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:01,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:01,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008641105.1_ASM864110v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:01,601] [INFO] Task started: Blastn
[2024-01-24 12:23:01,601] [INFO] Running command: blastn -query GCF_008641105.1_ASM864110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb23428d2-1f68-42fc-93ee-55a439a0bd55/dqc_reference/reference_markers_gtdb.fasta -out GCF_008641105.1_ASM864110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:03,105] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:03,109] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:03,110] [INFO] Target genome list was writen to GCF_008641105.1_ASM864110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:03,121] [INFO] Task started: fastANI
[2024-01-24 12:23:03,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg183a40c1-4fee-46a9-98dc-a722507d658e/GCF_008641105.1_ASM864110v1_genomic.fna.gz --refList GCF_008641105.1_ASM864110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008641105.1_ASM864110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:13,009] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:13,027] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:13,027] [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_008641105.1	s__Pseudomonas_D salina	100.0	1330	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_016763285.1	s__Pseudomonas_D sp016763285	81.0518	615	1399	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	80.009	573	1399	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_008365385.1	s__Pseudomonas_D laoshanensis	79.7381	537	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_000410875.1	s__Pseudomonas_D pelagia	79.5316	525	1399	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_002840055.1	s__Pseudomonas_D sp002840055	78.7625	356	1399	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_900114825.1	s__Pseudomonas_D yangmingensis	78.5031	335	1399	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_003444685.1	s__Pseudomonas_D gallaeciensis	78.4795	411	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.4794	290	1399	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_008638345.1	s__Pseudomonas_D saliphila	78.4609	361	1399	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	78.226	366	1399	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_012735335.1	s__Pseudomonas_D sp012735335	77.997	240	1399	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_000425625.1	s__Pseudomonas_N azotifigens	77.3356	228	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:13,029] [INFO] GTDB search result was written to GCF_008641105.1_ASM864110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:13,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:13,034] [INFO] DFAST_QC result json was written to GCF_008641105.1_ASM864110v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:13,034] [INFO] DFAST_QC completed!
[2024-01-24 12:23:13,034] [INFO] Total running time: 0h1m28s