[2024-01-24 13:17:33,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:33,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:33,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference
[2024-01-24 13:17:35,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,116] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,117] [INFO] Running command: gunzip -c /var/lib/cwl/stga89da96d-920b-4da0-b714-364beb074254/GCF_002236115.1_ASM223611v1_genomic.fna.gz | prodigal -d GCF_002236115.1_ASM223611v1_genomic.fna/cds.fna -a GCF_002236115.1_ASM223611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:02,837] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:02,837] [INFO] Task started: HMMsearch
[2024-01-24 13:18:02,837] [INFO] Running command: hmmsearch --tblout GCF_002236115.1_ASM223611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference/reference_markers.hmm GCF_002236115.1_ASM223611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:03,168] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:03,170] [INFO] Found 6/6 markers.
[2024-01-24 13:18:03,233] [INFO] Query marker FASTA was written to GCF_002236115.1_ASM223611v1_genomic.fna/markers.fasta
[2024-01-24 13:18:03,234] [INFO] Task started: Blastn
[2024-01-24 13:18:03,234] [INFO] Running command: blastn -query GCF_002236115.1_ASM223611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference/reference_markers.fasta -out GCF_002236115.1_ASM223611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:04,228] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:04,232] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:04,233] [INFO] Target genome list was writen to GCF_002236115.1_ASM223611v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:04,244] [INFO] Task started: fastANI
[2024-01-24 13:18:04,245] [INFO] Running command: fastANI --query /var/lib/cwl/stga89da96d-920b-4da0-b714-364beb074254/GCF_002236115.1_ASM223611v1_genomic.fna.gz --refList GCF_002236115.1_ASM223611v1_genomic.fna/target_genomes.txt --output GCF_002236115.1_ASM223611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:27,842] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:27,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:27,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:27,861] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:27,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:27,861] [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 jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	100.0	2173	2173	95	conclusive
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	92.4957	1767	2173	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	92.459	1758	2173	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	92.4434	1722	2173	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.9296	1542	2173	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	87.8049	1563	2173	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.7986	1486	2173	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.7944	1479	2173	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.5691	1574	2173	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	87.5016	1524	2173	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.3589	1395	2173	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.3396	1452	2173	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.5374	1425	2173	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.1763	1243	2173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:27,863] [INFO] DFAST Taxonomy check result was written to GCF_002236115.1_ASM223611v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:27,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:27,864] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:27,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference/checkm_data
[2024-01-24 13:18:27,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:27,924] [INFO] Task started: CheckM
[2024-01-24 13:18:27,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002236115.1_ASM223611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002236115.1_ASM223611v1_genomic.fna/checkm_input GCF_002236115.1_ASM223611v1_genomic.fna/checkm_result
[2024-01-24 13:19:40,027] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:40,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:40,051] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:40,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:40,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002236115.1_ASM223611v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:40,053] [INFO] Task started: Blastn
[2024-01-24 13:19:40,053] [INFO] Running command: blastn -query GCF_002236115.1_ASM223611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7f84b2-c8a8-4c48-8a12-d525c6eb53f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002236115.1_ASM223611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:41,788] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:41,794] [INFO] Selected 9 target genomes.
[2024-01-24 13:19:41,794] [INFO] Target genome list was writen to GCF_002236115.1_ASM223611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:41,805] [INFO] Task started: fastANI
[2024-01-24 13:19:41,806] [INFO] Running command: fastANI --query /var/lib/cwl/stga89da96d-920b-4da0-b714-364beb074254/GCF_002236115.1_ASM223611v1_genomic.fna.gz --refList GCF_002236115.1_ASM223611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002236115.1_ASM223611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:58,985] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:58,999] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:58,999] [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_002236115.1	s__Pseudomonas_E jessenii	100.0	2173	2173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	conclusive
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	94.2405	1734	2173	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_902498135.1	s__Pseudomonas_E fluorescens_BH	94.0695	1767	2173	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_001429045.1	s__Pseudomonas_E sp001429045	94.0662	1813	2173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002303925.1	s__Pseudomonas_E sp002303925	93.9199	1679	2173	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_000282455.1	s__Pseudomonas_E sp000282455	93.8398	1685	2173	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_003050925.1	s__Pseudomonas_E sp003050925	92.7276	1708	2173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.23	96.92	0.93	0.89	3	-
GCF_003053605.1	s__Pseudomonas_E sp003053605	92.6955	1692	2173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_002906155.1	s__Pseudomonas_E laurylsulfativorans	92.4512	1720	2173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:59,000] [INFO] GTDB search result was written to GCF_002236115.1_ASM223611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:59,001] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:59,004] [INFO] DFAST_QC result json was written to GCF_002236115.1_ASM223611v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:59,004] [INFO] DFAST_QC completed!
[2024-01-24 13:19:59,004] [INFO] Total running time: 0h2m25s