[2024-01-24 13:49:40,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference
[2024-01-24 13:49:42,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,001] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,001] [INFO] Running command: gunzip -c /var/lib/cwl/stgae0b7786-9683-4744-bf08-2f8dc9474b9d/GCF_009659625.1_ASM965962v1_genomic.fna.gz | prodigal -d GCF_009659625.1_ASM965962v1_genomic.fna/cds.fna -a GCF_009659625.1_ASM965962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:09,404] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:09,404] [INFO] Task started: HMMsearch
[2024-01-24 13:50:09,404] [INFO] Running command: hmmsearch --tblout GCF_009659625.1_ASM965962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference/reference_markers.hmm GCF_009659625.1_ASM965962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:09,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:09,747] [INFO] Found 6/6 markers.
[2024-01-24 13:50:09,800] [INFO] Query marker FASTA was written to GCF_009659625.1_ASM965962v1_genomic.fna/markers.fasta
[2024-01-24 13:50:09,800] [INFO] Task started: Blastn
[2024-01-24 13:50:09,800] [INFO] Running command: blastn -query GCF_009659625.1_ASM965962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference/reference_markers.fasta -out GCF_009659625.1_ASM965962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:10,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:10,669] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:10,669] [INFO] Target genome list was writen to GCF_009659625.1_ASM965962v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:10,685] [INFO] Task started: fastANI
[2024-01-24 13:50:10,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgae0b7786-9683-4744-bf08-2f8dc9474b9d/GCF_009659625.1_ASM965962v1_genomic.fna.gz --refList GCF_009659625.1_ASM965962v1_genomic.fna/target_genomes.txt --output GCF_009659625.1_ASM965962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:43,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:43,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:43,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:43,279] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:43,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:43,279] [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 synxantha	strain=DSM 18928	GCA_001439725.1	47883	47883	type	True	91.3083	1649	1994	95	below_threshold
Pseudomonas synxantha	strain=NBRC 3913	GCA_002091795.1	47883	47883	type	True	91.233	1651	1994	95	below_threshold
Pseudomonas synxantha	strain=LMG 2190	GCA_900105675.1	47883	47883	type	True	91.1912	1694	1994	95	below_threshold
Pseudomonas synxantha	strain=NCTC10696	GCA_901482615.1	47883	47883	type	True	91.1795	1679	1994	95	below_threshold
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	91.1155	1658	1994	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	90.2572	1643	1994	95	below_threshold
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	90.135	1619	1994	95	below_threshold
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	90.1142	1683	1994	95	below_threshold
Pseudomonas paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	90.0912	1635	1994	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.3411	1526	1994	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	88.2215	1563	1994	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.1062	1578	1994	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.958	1539	1994	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.9359	1477	1994	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.3007	1284	1994	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	83.4359	1243	1994	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	79.4232	846	1994	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	79.4166	846	1994	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	79.4116	852	1994	95	below_threshold
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	77.5819	212	1994	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	76.0976	98	1994	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	75.3303	69	1994	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:43,281] [INFO] DFAST Taxonomy check result was written to GCF_009659625.1_ASM965962v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:43,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:43,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:43,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference/checkm_data
[2024-01-24 13:50:43,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:43,336] [INFO] Task started: CheckM
[2024-01-24 13:50:43,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009659625.1_ASM965962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009659625.1_ASM965962v1_genomic.fna/checkm_input GCF_009659625.1_ASM965962v1_genomic.fna/checkm_result
[2024-01-24 13:51:54,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:54,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:54,441] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:54,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:54,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009659625.1_ASM965962v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:54,442] [INFO] Task started: Blastn
[2024-01-24 13:51:54,442] [INFO] Running command: blastn -query GCF_009659625.1_ASM965962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg379eec61-d6f3-4966-aaf5-e4c2c1c5855d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009659625.1_ASM965962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:55,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:55,813] [INFO] Selected 21 target genomes.
[2024-01-24 13:51:55,813] [INFO] Target genome list was writen to GCF_009659625.1_ASM965962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:55,929] [INFO] Task started: fastANI
[2024-01-24 13:51:55,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgae0b7786-9683-4744-bf08-2f8dc9474b9d/GCF_009659625.1_ASM965962v1_genomic.fna.gz --refList GCF_009659625.1_ASM965962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009659625.1_ASM965962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:27,573] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:27,592] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:27,592] [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_009659625.1	s__Pseudomonas_E haemolytica	100.0	1993	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	conclusive
GCF_900105675.1	s__Pseudomonas_E synxantha	91.1903	1694	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_003851495.1	s__Pseudomonas_E fluorescens_BB	91.117	1663	1994	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_001439685.1	s__Pseudomonas_E libanensis	91.1155	1658	1994	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_000263715.2	s__Pseudomonas_E synxantha_A	90.5074	1682	1994	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_001902145.1	s__Pseudomonas_E fluorescens_BV	90.1964	1617	1994	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	90.1391	1619	1994	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_001439845.1	s__Pseudomonas_E lactis	90.0976	1687	1994	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_904063055.1	s__Pseudomonas_E paracarnis	90.0953	1635	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	-
GCF_000612585.1	s__Pseudomonas_E sp000612585	88.315	1507	1994	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_002934065.1	s__Pseudomonas_E orientalis_A	88.1856	1531	1994	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_002007785.1	s__Pseudomonas_E azotoformans_B	88.1517	1556	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.86	0.94	0.92	6	-
GCF_003612935.1	s__Pseudomonas_E sp003013355	88.135	1570	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.56	0.95	0.92	7	-
GCF_002563895.1	s__Pseudomonas_E lurida	87.9695	1538	1994	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_001186335.1	s__Pseudomonas_E trivialis_B	87.8847	1560	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_019139815.1	s__Pseudomonas_E sp900005815	87.7396	1471	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_001983175.1	s__Pseudomonas_E cedrina	87.5129	1481	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_004519405.1	s__Pseudomonas_E sp004519405	87.2618	1548	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.60	98.40	0.98	0.92	5	-
GCF_002018875.1	s__Pseudomonas_E sp002018875	83.7098	1315	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.08	96.52	0.93	0.90	4	-
GCF_000746525.1	s__Pseudomonas_E alkylphenolica	81.3998	945	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.61	96.52	0.84	0.83	3	-
GCA_016716465.1	s__JADJWH01 sp016716465	75.6153	62	1994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:27,594] [INFO] GTDB search result was written to GCF_009659625.1_ASM965962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:27,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:27,599] [INFO] DFAST_QC result json was written to GCF_009659625.1_ASM965962v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:27,599] [INFO] DFAST_QC completed!
[2024-01-24 13:52:27,599] [INFO] Total running time: 0h2m47s