[2024-01-25 19:34:21,085] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference
[2024-01-25 19:34:22,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,210] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f7e2efb-e4a7-43bb-bb4e-303993f7d0a4/GCF_017114825.1_ASM1711482v1_genomic.fna.gz | prodigal -d GCF_017114825.1_ASM1711482v1_genomic.fna/cds.fna -a GCF_017114825.1_ASM1711482v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:37,909] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:37,909] [INFO] Task started: HMMsearch
[2024-01-25 19:34:37,909] [INFO] Running command: hmmsearch --tblout GCF_017114825.1_ASM1711482v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference/reference_markers.hmm GCF_017114825.1_ASM1711482v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:38,172] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:38,173] [INFO] Found 6/6 markers.
[2024-01-25 19:34:38,218] [INFO] Query marker FASTA was written to GCF_017114825.1_ASM1711482v1_genomic.fna/markers.fasta
[2024-01-25 19:34:38,218] [INFO] Task started: Blastn
[2024-01-25 19:34:38,218] [INFO] Running command: blastn -query GCF_017114825.1_ASM1711482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference/reference_markers.fasta -out GCF_017114825.1_ASM1711482v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:39,086] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:39,089] [INFO] Selected 17 target genomes.
[2024-01-25 19:34:39,089] [INFO] Target genome list was writen to GCF_017114825.1_ASM1711482v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:39,093] [INFO] Task started: fastANI
[2024-01-25 19:34:39,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f7e2efb-e4a7-43bb-bb4e-303993f7d0a4/GCF_017114825.1_ASM1711482v1_genomic.fna.gz --refList GCF_017114825.1_ASM1711482v1_genomic.fna/target_genomes.txt --output GCF_017114825.1_ASM1711482v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:04,856] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:04,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:04,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:04,867] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:35:04,867] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:35:04,867] [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 mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	86.4751	1398	1870	95	below_threshold
Pseudomonas mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	86.4502	1425	1870	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	86.4407	1390	1870	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	85.9996	1301	1870	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	85.9507	1298	1870	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	85.8987	1303	1870	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	85.7175	1320	1870	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	85.6064	1330	1870	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	85.5824	1372	1870	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	85.5182	1341	1870	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	85.4897	1326	1870	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	85.4486	1370	1870	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	85.388	1410	1870	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.0247	1299	1870	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.012	1274	1870	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	84.4766	1308	1870	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	83.6287	1164	1870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:04,871] [INFO] DFAST Taxonomy check result was written to GCF_017114825.1_ASM1711482v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:04,872] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:04,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:04,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference/checkm_data
[2024-01-25 19:35:04,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:04,930] [INFO] Task started: CheckM
[2024-01-25 19:35:04,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017114825.1_ASM1711482v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017114825.1_ASM1711482v1_genomic.fna/checkm_input GCF_017114825.1_ASM1711482v1_genomic.fna/checkm_result
[2024-01-25 19:35:50,680] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:50,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:50,720] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:50,720] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:50,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017114825.1_ASM1711482v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:50,722] [INFO] Task started: Blastn
[2024-01-25 19:35:50,722] [INFO] Running command: blastn -query GCF_017114825.1_ASM1711482v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25925cae-7877-461f-87ca-297f0cc786ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_017114825.1_ASM1711482v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:52,477] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:52,481] [INFO] Selected 26 target genomes.
[2024-01-25 19:35:52,481] [INFO] Target genome list was writen to GCF_017114825.1_ASM1711482v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:52,509] [INFO] Task started: fastANI
[2024-01-25 19:35:52,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f7e2efb-e4a7-43bb-bb4e-303993f7d0a4/GCF_017114825.1_ASM1711482v1_genomic.fna.gz --refList GCF_017114825.1_ASM1711482v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017114825.1_ASM1711482v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:33,246] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:33,264] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:33,265] [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_017114825.1	s__Pseudomonas_E gregormendelii	100.0	1866	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.47	97.13	0.88	0.86	8	conclusive
GCF_000282415.1	s__Pseudomonas_E sp000282415	86.6239	1314	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.21	0.89	0.87	6	-
GCF_018502625.1	s__Pseudomonas_E fluorescens_BW	86.5744	1407	1870	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_003151075.1	s__Pseudomonas_E sp003151075	86.5687	1404	1870	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_001297125.1	s__Pseudomonas_E sp001297125	86.5606	1412	1870	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_006094435.1	s__Pseudomonas_E sp002029345	86.5097	1416	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.75	98.73	0.83	0.83	3	-
GCF_006438925.1	s__Pseudomonas_E mandelii_C	86.4656	1346	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	96.81	0.87	0.83	4	-
GCF_902497855.1	s__Pseudomonas_E fluorescens_BI	86.45	1411	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.52	95.78	0.88	0.82	3	-
GCF_004136015.1	s__Pseudomonas_E sp004136015	86.3755	1381	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.14	95.84	0.91	0.90	3	-
GCF_008370045.1	s__Pseudomonas_E sp008370045	86.3716	1410	1870	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_004364415.1	s__Pseudomonas_E mandelii_D	86.3699	1377	1870	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_900105495.1	s__Pseudomonas_E frederiksbergensis	86.3117	1330	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.60	0.93	0.91	12	-
GCF_018449725.1	s__Pseudomonas_E sp018449725	86.2275	1378	1870	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_009761815.1	s__Pseudomonas_E sp009761815	86.1554	1321	1870	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_015461845.1	s__Pseudomonas_E mucoides	86.0398	1370	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.43	0.93	0.92	3	-
GCF_000282195.1	s__Pseudomonas_E sp000282195	86.0235	1263	1870	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_000282495.1	s__Pseudomonas_E sp000282495	85.8869	1273	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.96	0.87	0.86	6	-
GCF_000802965.1	s__Pseudomonas_E fluorescens_A	85.8016	1358	1870	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_000282475.1	s__Pseudomonas_E sp000282475	85.7575	1347	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_001984065.1	s__Pseudomonas_E sp001984065	85.7125	1305	1870	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	85.666	1372	1870	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_002934665.1	s__Pseudomonas_E laurylsulfatiphila	85.5988	1370	1870	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_001976065.1	s__Pseudomonas_E putida_G	85.5688	1427	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.91	0.91	2	-
GCF_001945365.1	s__Pseudomonas_E reinekei	85.5674	1346	1870	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_902497845.1	s__Pseudomonas_E fluorescens_BN	85.4985	1379	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.81	0.91	0.91	2	-
GCF_900105115.1	s__Pseudomonas_E mohnii	85.4498	1366	1870	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	96.18	0.85	0.79	7	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:33,267] [INFO] GTDB search result was written to GCF_017114825.1_ASM1711482v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:33,267] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:33,271] [INFO] DFAST_QC result json was written to GCF_017114825.1_ASM1711482v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:33,271] [INFO] DFAST_QC completed!
[2024-01-25 19:36:33,271] [INFO] Total running time: 0h2m12s