[2024-01-24 14:14:31,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:31,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:31,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference
[2024-01-24 14:14:32,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:32,854] [INFO] Task started: Prodigal
[2024-01-24 14:14:32,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgb02e2b20-91e7-4617-92cd-57b7fcfa30bb/GCF_904063055.1_V5_genomic.fna.gz | prodigal -d GCF_904063055.1_V5_genomic.fna/cds.fna -a GCF_904063055.1_V5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:54,920] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:54,920] [INFO] Task started: HMMsearch
[2024-01-24 14:14:54,920] [INFO] Running command: hmmsearch --tblout GCF_904063055.1_V5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference/reference_markers.hmm GCF_904063055.1_V5_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:55,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:55,316] [INFO] Found 6/6 markers.
[2024-01-24 14:14:55,370] [INFO] Query marker FASTA was written to GCF_904063055.1_V5_genomic.fna/markers.fasta
[2024-01-24 14:14:55,370] [INFO] Task started: Blastn
[2024-01-24 14:14:55,370] [INFO] Running command: blastn -query GCF_904063055.1_V5_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference/reference_markers.fasta -out GCF_904063055.1_V5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:56,259] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:56,263] [INFO] Selected 19 target genomes.
[2024-01-24 14:14:56,263] [INFO] Target genome list was writen to GCF_904063055.1_V5_genomic.fna/target_genomes.txt
[2024-01-24 14:14:56,274] [INFO] Task started: fastANI
[2024-01-24 14:14:56,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgb02e2b20-91e7-4617-92cd-57b7fcfa30bb/GCF_904063055.1_V5_genomic.fna.gz --refList GCF_904063055.1_V5_genomic.fna/target_genomes.txt --output GCF_904063055.1_V5_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:22,253] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:22,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:22,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:22,275] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:22,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:22,275] [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 paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	100.0	2007	2008	95	conclusive
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	94.9863	1777	2008	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	94.6774	1758	2008	95	below_threshold
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	91.0449	1674	2008	95	below_threshold
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	90.258	1641	2008	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.0663	1530	2008	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.7498	1562	2008	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	87.5942	1545	2008	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	87.5458	1536	2008	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.5313	1548	2008	95	below_threshold
Pseudomonas palleroniana	strain=LMG 23076	GCA_003031675.1	191390	191390	type	True	87.2053	1502	2008	95	below_threshold
Pseudomonas palleroniana	strain=CCUG 51524	GCA_008801495.1	191390	191390	type	True	87.1565	1509	2008	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.7547	1435	2008	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.0341	1295	2008	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	76.3319	81	2008	95	below_threshold
Ferrimonas sediminicola	strain=IMCC35001	GCA_005116715.1	2569538	2569538	type	True	75.9918	89	2008	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	75.8258	150	2008	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	75.8052	154	2008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:22,277] [INFO] DFAST Taxonomy check result was written to GCF_904063055.1_V5_genomic.fna/tc_result.tsv
[2024-01-24 14:15:22,277] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:22,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:22,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference/checkm_data
[2024-01-24 14:15:22,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:22,333] [INFO] Task started: CheckM
[2024-01-24 14:15:22,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_904063055.1_V5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_904063055.1_V5_genomic.fna/checkm_input GCF_904063055.1_V5_genomic.fna/checkm_result
[2024-01-24 14:16:28,282] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:28,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:28,303] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:28,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:28,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_904063055.1_V5_genomic.fna/markers.fasta)
[2024-01-24 14:16:28,304] [INFO] Task started: Blastn
[2024-01-24 14:16:28,304] [INFO] Running command: blastn -query GCF_904063055.1_V5_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e4b5f77-2e4f-43f7-bf70-56b5a63a5c4c/dqc_reference/reference_markers_gtdb.fasta -out GCF_904063055.1_V5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:29,871] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:29,876] [INFO] Selected 16 target genomes.
[2024-01-24 14:16:29,876] [INFO] Target genome list was writen to GCF_904063055.1_V5_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:29,912] [INFO] Task started: fastANI
[2024-01-24 14:16:29,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgb02e2b20-91e7-4617-92cd-57b7fcfa30bb/GCF_904063055.1_V5_genomic.fna.gz --refList GCF_904063055.1_V5_genomic.fna/target_genomes_gtdb.txt --output GCF_904063055.1_V5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:56,838] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:56,852] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:56,853] [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_904063055.1	s__Pseudomonas_E paracarnis	100.0	2007	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	conclusive
GCF_001439845.1	s__Pseudomonas_E lactis	94.9863	1777	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_001902145.1	s__Pseudomonas_E fluorescens_BV	94.8543	1669	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.76	95.23	0.87	0.84	22	-
GCF_001439735.1	s__Pseudomonas_E paralactis	91.0494	1674	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	90.4657	1672	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_001439685.1	s__Pseudomonas_E libanensis	90.2617	1640	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	97.93	95.87	0.95	0.89	3	-
GCF_009659625.1	s__Pseudomonas_E haemolytica	90.1133	1638	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_003851495.1	s__Pseudomonas_E fluorescens_BB	89.7846	1656	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3929	98.85	97.70	0.94	0.89	3	-
GCF_002934065.1	s__Pseudomonas_E orientalis_A	88.2547	1561	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.15	95.96	0.86	0.83	21	-
GCF_900591205.1	s__Pseudomonas_E sp900591205	87.8672	1500	2008	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_002022265.1	s__Pseudomonas_E fluorescens_C	87.5638	1520	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.28	96.98	0.88	0.86	8	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	87.5479	1571	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_002563895.1	s__Pseudomonas_E lurida	87.536	1548	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_005116715.1	s__Ferrimonas sp005116715	75.9918	89	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Ferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	75.8052	154	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002726615.1	s__Marinobacter sp002726615	75.7611	51	2008	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:56,855] [INFO] GTDB search result was written to GCF_904063055.1_V5_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:56,856] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:56,860] [INFO] DFAST_QC result json was written to GCF_904063055.1_V5_genomic.fna/dqc_result.json
[2024-01-24 14:16:56,860] [INFO] DFAST_QC completed!
[2024-01-24 14:16:56,860] [INFO] Total running time: 0h2m25s