[2024-01-25 20:13:35,803] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference
[2024-01-25 20:13:37,079] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:37,080] [INFO] Task started: Prodigal
[2024-01-25 20:13:37,080] [INFO] Running command: gunzip -c /var/lib/cwl/stgcde515ae-8d8e-4bca-b457-22acb8c0893f/GCF_002056295.1_ASM205629v1_genomic.fna.gz | prodigal -d GCF_002056295.1_ASM205629v1_genomic.fna/cds.fna -a GCF_002056295.1_ASM205629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:48,074] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:48,074] [INFO] Task started: HMMsearch
[2024-01-25 20:13:48,074] [INFO] Running command: hmmsearch --tblout GCF_002056295.1_ASM205629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference/reference_markers.hmm GCF_002056295.1_ASM205629v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:48,342] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:48,343] [INFO] Found 6/6 markers.
[2024-01-25 20:13:48,388] [INFO] Query marker FASTA was written to GCF_002056295.1_ASM205629v1_genomic.fna/markers.fasta
[2024-01-25 20:13:48,388] [INFO] Task started: Blastn
[2024-01-25 20:13:48,388] [INFO] Running command: blastn -query GCF_002056295.1_ASM205629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference/reference_markers.fasta -out GCF_002056295.1_ASM205629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:49,307] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:49,311] [INFO] Selected 20 target genomes.
[2024-01-25 20:13:49,311] [INFO] Target genome list was writen to GCF_002056295.1_ASM205629v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:49,325] [INFO] Task started: fastANI
[2024-01-25 20:13:49,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgcde515ae-8d8e-4bca-b457-22acb8c0893f/GCF_002056295.1_ASM205629v1_genomic.fna.gz --refList GCF_002056295.1_ASM205629v1_genomic.fna/target_genomes.txt --output GCF_002056295.1_ASM205629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:05,340] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:05,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:05,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:05,355] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:14:05,355] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:14:05,355] [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	80.3017	525	1345	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.8384	547	1345	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	79.7728	565	1345	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	79.759	589	1345	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	79.6999	594	1345	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	79.6789	477	1345	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	79.6645	484	1345	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	79.1866	441	1345	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	79.1735	459	1345	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.9124	443	1345	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.7856	390	1345	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.6464	396	1345	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	78.6464	425	1345	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.548	402	1345	95	below_threshold
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	78.4266	426	1345	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	78.2511	412	1345	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	78.2414	413	1345	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	78.1949	418	1345	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	78.1042	338	1345	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	78.0676	320	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:05,357] [INFO] DFAST Taxonomy check result was written to GCF_002056295.1_ASM205629v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:05,358] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:05,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:05,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference/checkm_data
[2024-01-25 20:14:05,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:05,409] [INFO] Task started: CheckM
[2024-01-25 20:14:05,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002056295.1_ASM205629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002056295.1_ASM205629v1_genomic.fna/checkm_input GCF_002056295.1_ASM205629v1_genomic.fna/checkm_result
[2024-01-25 20:14:39,307] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:39,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:39,326] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:39,326] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:39,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002056295.1_ASM205629v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:39,327] [INFO] Task started: Blastn
[2024-01-25 20:14:39,327] [INFO] Running command: blastn -query GCF_002056295.1_ASM205629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d3b7ea1-cc40-419d-a53e-1d8b9f76124f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002056295.1_ASM205629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:40,919] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:40,923] [INFO] Selected 17 target genomes.
[2024-01-25 20:14:40,923] [INFO] Target genome list was writen to GCF_002056295.1_ASM205629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:40,952] [INFO] Task started: fastANI
[2024-01-25 20:14:40,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgcde515ae-8d8e-4bca-b457-22acb8c0893f/GCF_002056295.1_ASM205629v1_genomic.fna.gz --refList GCF_002056295.1_ASM205629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002056295.1_ASM205629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:54,462] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:54,473] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:54,474] [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	98.6578	1176	1345	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	80.2794	527	1345	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	80.1345	599	1345	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	79.9431	562	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_900115905.1	s__Pseudomonas_D formosensis	79.9325	511	1345	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_002979975.1	s__Pseudomonas_D sp002979975	79.9016	584	1345	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_000939975.1	s__Pseudomonas_D saudimassiliensis	79.8705	505	1345	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_900114765.1	s__Pseudomonas_D pachastrellae	79.7728	565	1345	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_002197985.1	s__Pseudomonas_D aestusnigri	79.7182	592	1345	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	79.6842	476	1345	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	79.5545	394	1345	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	79.3241	348	1345	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	79.2343	451	1345	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_900105005.1	s__Pseudomonas_D litoralis	79.1825	461	1345	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	79.147	465	1345	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	79.0259	515	1345	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_016763285.1	s__Pseudomonas_D sp016763285	78.4595	348	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:54,476] [INFO] GTDB search result was written to GCF_002056295.1_ASM205629v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:54,477] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:54,481] [INFO] DFAST_QC result json was written to GCF_002056295.1_ASM205629v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:54,481] [INFO] DFAST_QC completed!
[2024-01-25 20:14:54,481] [INFO] Total running time: 0h1m19s