[2024-01-24 12:05:50,436] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:50,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:50,438] [INFO] DQC Reference Directory: /var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference
[2024-01-24 12:05:52,739] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:52,740] [INFO] Task started: Prodigal
[2024-01-24 12:05:52,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d2e0f71-e082-43bf-9c01-bfd23f55ea08/GCF_014174475.1_ASM1417447v1_genomic.fna.gz | prodigal -d GCF_014174475.1_ASM1417447v1_genomic.fna/cds.fna -a GCF_014174475.1_ASM1417447v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:07,212] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:07,212] [INFO] Task started: HMMsearch
[2024-01-24 12:06:07,213] [INFO] Running command: hmmsearch --tblout GCF_014174475.1_ASM1417447v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference/reference_markers.hmm GCF_014174475.1_ASM1417447v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:07,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:07,430] [INFO] Found 6/6 markers.
[2024-01-24 12:06:07,470] [INFO] Query marker FASTA was written to GCF_014174475.1_ASM1417447v1_genomic.fna/markers.fasta
[2024-01-24 12:06:07,470] [INFO] Task started: Blastn
[2024-01-24 12:06:07,470] [INFO] Running command: blastn -query GCF_014174475.1_ASM1417447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference/reference_markers.fasta -out GCF_014174475.1_ASM1417447v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:08,485] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:08,489] [INFO] Selected 16 target genomes.
[2024-01-24 12:06:08,489] [INFO] Target genome list was writen to GCF_014174475.1_ASM1417447v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:08,515] [INFO] Task started: fastANI
[2024-01-24 12:06:08,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2e0f71-e082-43bf-9c01-bfd23f55ea08/GCF_014174475.1_ASM1417447v1_genomic.fna.gz --refList GCF_014174475.1_ASM1417447v1_genomic.fna/target_genomes.txt --output GCF_014174475.1_ASM1417447v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:25,702] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:25,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:25,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:25,717] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:25,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:25,718] [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 ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	100.0	1535	1535	95	conclusive
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	86.7788	1102	1535	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	86.6132	1076	1535	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	85.6614	1047	1535	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	85.6376	1060	1535	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	83.5348	948	1535	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	83.4883	957	1535	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.3781	879	1535	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	83.2804	1001	1535	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	83.2599	955	1535	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	83.1687	955	1535	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	83.0745	957	1535	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	82.3797	849	1535	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.2112	709	1535	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	81.9665	819	1535	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	81.917	813	1535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:25,721] [INFO] DFAST Taxonomy check result was written to GCF_014174475.1_ASM1417447v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:25,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:25,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:25,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference/checkm_data
[2024-01-24 12:06:25,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:25,793] [INFO] Task started: CheckM
[2024-01-24 12:06:25,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174475.1_ASM1417447v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174475.1_ASM1417447v1_genomic.fna/checkm_input GCF_014174475.1_ASM1417447v1_genomic.fna/checkm_result
[2024-01-24 12:07:08,906] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:08,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:08,930] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:08,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:08,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174475.1_ASM1417447v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:08,931] [INFO] Task started: Blastn
[2024-01-24 12:07:08,931] [INFO] Running command: blastn -query GCF_014174475.1_ASM1417447v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeadfbfe7-c37e-4f08-9240-2e65ccf1a3c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174475.1_ASM1417447v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:11,022] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:11,025] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:11,025] [INFO] Target genome list was writen to GCF_014174475.1_ASM1417447v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:11,042] [INFO] Task started: fastANI
[2024-01-24 12:07:11,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d2e0f71-e082-43bf-9c01-bfd23f55ea08/GCF_014174475.1_ASM1417447v1_genomic.fna.gz --refList GCF_014174475.1_ASM1417447v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174475.1_ASM1417447v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:27,374] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:27,391] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:27,392] [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_014174475.1	s__Pseudomonas_E sp014174475	100.0	1535	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	87.8279	1190	1535	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_009799925.1	s__Pseudomonas_E sp009799925	87.1534	1061	1535	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_902506505.1	s__Pseudomonas_E sp902506505	87.0123	1032	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_013200955.2	s__Pseudomonas_E campi	86.7962	1100	1535	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_014164785.1	s__Pseudomonas_E sp014164785	86.6083	1076	1535	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_014851905.1	s__Pseudomonas_E sp014851905	86.0483	1096	1535	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_001592875.1	s__Pseudomonas_E sp001592875	85.1081	1070	1535	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_014851865.1	s__Pseudomonas_E sp014851865	84.4615	1006	1535	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_904061905.1	s__Pseudomonas_E carbonaria	83.2542	956	1535	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_004327355.1	s__Pseudomonas_E dryadis	82.6861	894	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	82.4395	959	1535	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001839655.1	s__Pseudomonas_E argentinensis_B	82.3081	814	1535	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_001945395.1	s__Pseudomonas_E sp001945395	81.7528	806	1535	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 12:07:27,393] [INFO] GTDB search result was written to GCF_014174475.1_ASM1417447v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:27,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:27,399] [INFO] DFAST_QC result json was written to GCF_014174475.1_ASM1417447v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:27,399] [INFO] DFAST_QC completed!
[2024-01-24 12:07:27,399] [INFO] Total running time: 0h1m37s