[2024-01-24 13:03:20,665] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,667] [INFO] DQC Reference Directory: /var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference
[2024-01-24 13:03:21,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:21,879] [INFO] Task started: Prodigal
[2024-01-24 13:03:21,879] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8cea263-ddea-4736-ba60-bb16f382f7bd/GCF_029504145.1_ASM2950414v1_genomic.fna.gz | prodigal -d GCF_029504145.1_ASM2950414v1_genomic.fna/cds.fna -a GCF_029504145.1_ASM2950414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:43,722] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:43,723] [INFO] Task started: HMMsearch
[2024-01-24 13:03:43,723] [INFO] Running command: hmmsearch --tblout GCF_029504145.1_ASM2950414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference/reference_markers.hmm GCF_029504145.1_ASM2950414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:44,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:44,061] [INFO] Found 6/6 markers.
[2024-01-24 13:03:44,120] [INFO] Query marker FASTA was written to GCF_029504145.1_ASM2950414v1_genomic.fna/markers.fasta
[2024-01-24 13:03:44,121] [INFO] Task started: Blastn
[2024-01-24 13:03:44,121] [INFO] Running command: blastn -query GCF_029504145.1_ASM2950414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference/reference_markers.fasta -out GCF_029504145.1_ASM2950414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:45,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:45,045] [INFO] Selected 20 target genomes.
[2024-01-24 13:03:45,046] [INFO] Target genome list was writen to GCF_029504145.1_ASM2950414v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:45,055] [INFO] Task started: fastANI
[2024-01-24 13:03:45,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8cea263-ddea-4736-ba60-bb16f382f7bd/GCF_029504145.1_ASM2950414v1_genomic.fna.gz --refList GCF_029504145.1_ASM2950414v1_genomic.fna/target_genomes.txt --output GCF_029504145.1_ASM2950414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:04:14,669] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:14,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:04:14,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:04:14,688] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:04:14,688] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:04:14,689] [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 laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	92.4218	1661	2189	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	92.4147	1651	2189	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	92.3915	1631	2189	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	91.8589	1653	2189	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	87.7459	1456	2189	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.6815	1535	2189	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.6375	1444	2189	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.4553	1434	2189	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.4056	1441	2189	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	87.3809	1493	2189	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	86.883	1419	2189	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.2885	1364	2189	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.2095	1322	2189	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.5425	1343	2189	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.2013	1199	2189	95	below_threshold
Pseudomonas synxantha	strain=LMG 2190	GCA_900105675.1	47883	47883	type	True	83.1432	1127	2189	95	below_threshold
Pseudomonas synxantha	strain=NCTC10696	GCA_901482615.1	47883	47883	type	True	83.1041	1137	2189	95	below_threshold
Pseudomonas synxantha	strain=DSM 18928	GCA_001439725.1	47883	47883	type	True	83.0522	1117	2189	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	80.0439	703	2189	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	79.9207	682	2189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:04:14,690] [INFO] DFAST Taxonomy check result was written to GCF_029504145.1_ASM2950414v1_genomic.fna/tc_result.tsv
[2024-01-24 13:04:14,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:04:14,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:04:14,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference/checkm_data
[2024-01-24 13:04:14,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:04:15,010] [INFO] Task started: CheckM
[2024-01-24 13:04:15,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029504145.1_ASM2950414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029504145.1_ASM2950414v1_genomic.fna/checkm_input GCF_029504145.1_ASM2950414v1_genomic.fna/checkm_result
[2024-01-24 13:05:18,563] [INFO] Task succeeded: CheckM
[2024-01-24 13:05:18,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:05:18,593] [INFO] ===== Completeness check finished =====
[2024-01-24 13:05:18,593] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:05:18,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029504145.1_ASM2950414v1_genomic.fna/markers.fasta)
[2024-01-24 13:05:18,594] [INFO] Task started: Blastn
[2024-01-24 13:05:18,595] [INFO] Running command: blastn -query GCF_029504145.1_ASM2950414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde7f0a52-4d99-4c63-9dbc-4b96d8afa203/dqc_reference/reference_markers_gtdb.fasta -out GCF_029504145.1_ASM2950414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:05:19,986] [INFO] Task succeeded: Blastn
[2024-01-24 13:05:19,992] [INFO] Selected 18 target genomes.
[2024-01-24 13:05:19,992] [INFO] Target genome list was writen to GCF_029504145.1_ASM2950414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:05:20,007] [INFO] Task started: fastANI
[2024-01-24 13:05:20,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8cea263-ddea-4736-ba60-bb16f382f7bd/GCF_029504145.1_ASM2950414v1_genomic.fna.gz --refList GCF_029504145.1_ASM2950414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029504145.1_ASM2950414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:05:49,831] [INFO] Task succeeded: fastANI
[2024-01-24 13:05:49,852] [INFO] Found 18 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:05:49,853] [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_003053605.1	s__Pseudomonas_E sp003053605	96.0394	1743	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	inconclusive
GCF_016909445.1	s__Pseudomonas_E stutzeri_A	95.1269	1668	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	inconclusive
GCF_000282455.1	s__Pseudomonas_E sp000282455	92.8589	1546	2189	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_902498135.1	s__Pseudomonas_E fluorescens_BH	92.6871	1613	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	92.581	1609	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_002934665.1	s__Pseudomonas_E laurylsulfatiphila	92.4311	1660	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.74	0.86	0.82	13	-
GCF_002236115.1	s__Pseudomonas_E jessenii	92.3913	1631	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_002113025.1	s__Pseudomonas_E sp002113025	92.2009	1617	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.31	95.23	0.87	0.84	4	-
GCF_002303925.1	s__Pseudomonas_E sp002303925	92.1255	1581	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_002906155.1	s__Pseudomonas_E laurylsulfativorans	91.8589	1653	2189	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_009764265.1	s__Pseudomonas_E sp009764265	91.5824	1573	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.48	95.48	0.85	0.85	2	-
GCF_001945365.1	s__Pseudomonas_E reinekei	87.4389	1436	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	95.43	0.93	0.85	5	-
GCF_900105115.1	s__Pseudomonas_E mohnii	87.401	1490	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	96.18	0.85	0.79	7	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	85.643	1328	2189	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_013386165.1	s__Pseudomonas_E gingeri_C	83.3963	1178	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.31	0.93	0.92	4	-
GCF_018417635.1	s__Pseudomonas_E sp900101695	82.2556	1056	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.49	97.27	0.95	0.94	5	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	79.9443	679	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_019090095.1	s__Pseudomonas_A stutzeri_AN	78.8262	510	2189	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:05:50,050] [INFO] GTDB search result was written to GCF_029504145.1_ASM2950414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:05:50,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:05:50,055] [INFO] DFAST_QC result json was written to GCF_029504145.1_ASM2950414v1_genomic.fna/dqc_result.json
[2024-01-24 13:05:50,055] [INFO] DFAST_QC completed!
[2024-01-24 13:05:50,055] [INFO] Total running time: 0h2m29s