[2024-01-24 13:49:55,658] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference
[2024-01-24 13:49:56,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,965] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,965] [INFO] Running command: gunzip -c /var/lib/cwl/stga273cc6b-2967-4c03-abb3-dd6e90ff170e/GCF_014236655.1_ASM1423665v1_genomic.fna.gz | prodigal -d GCF_014236655.1_ASM1423665v1_genomic.fna/cds.fna -a GCF_014236655.1_ASM1423665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,220] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,220] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,221] [INFO] Running command: hmmsearch --tblout GCF_014236655.1_ASM1423665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference/reference_markers.hmm GCF_014236655.1_ASM1423665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:17,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:17,580] [INFO] Found 6/6 markers.
[2024-01-24 13:50:17,637] [INFO] Query marker FASTA was written to GCF_014236655.1_ASM1423665v1_genomic.fna/markers.fasta
[2024-01-24 13:50:17,637] [INFO] Task started: Blastn
[2024-01-24 13:50:17,637] [INFO] Running command: blastn -query GCF_014236655.1_ASM1423665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference/reference_markers.fasta -out GCF_014236655.1_ASM1423665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:18,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:18,559] [INFO] Selected 28 target genomes.
[2024-01-24 13:50:18,559] [INFO] Target genome list was writen to GCF_014236655.1_ASM1423665v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:18,580] [INFO] Task started: fastANI
[2024-01-24 13:50:18,581] [INFO] Running command: fastANI --query /var/lib/cwl/stga273cc6b-2967-4c03-abb3-dd6e90ff170e/GCF_014236655.1_ASM1423665v1_genomic.fna.gz --refList GCF_014236655.1_ASM1423665v1_genomic.fna/target_genomes.txt --output GCF_014236655.1_ASM1423665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:54,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:54,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:54,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:55,007] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:55,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:55,008] [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 kielensis	strain=MBT-1	GCA_014236655.1	2762577	2762577	type	True	100.0	1957	1961	95	conclusive
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	85.4668	1282	1961	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	85.4464	1287	1961	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	85.413	1245	1961	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	85.4127	1317	1961	95	below_threshold
Pseudomonas mandelii	strain=DSM 17967	GCA_007858265.1	75612	75612	suspected-type	True	85.3879	1307	1961	95	below_threshold
Pseudomonas mandelii	strain=LMG 21607	GCA_900106065.1	75612	75612	suspected-type	True	85.3798	1320	1961	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	85.3648	1285	1961	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	85.3516	1237	1961	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	85.3205	1299	1961	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	85.3165	1253	1961	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.1802	1209	1961	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.1707	1207	1961	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	85.1278	1238	1961	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	85.1175	1244	1961	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	85.0523	1247	1961	95	below_threshold
Pseudomonas umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	84.8839	1305	1961	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	84.4561	1222	1961	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	84.1948	1148	1961	95	below_threshold
Pseudomonas azotoformans	strain=LMG 21611	GCA_900103345.1	47878	47878	suspected-type	True	84.1171	1169	1961	95	below_threshold
Pseudomonas azotoformans		GCA_900624915.1	47878	47878	suspected-type	True	84.0729	1169	1961	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	83.962	1158	1961	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	83.4748	1051	1961	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.6472	852	1961	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	82.0272	926	1961	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	81.3995	835	1961	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	81.395	835	1961	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	79.1238	545	1961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:55,009] [INFO] DFAST Taxonomy check result was written to GCF_014236655.1_ASM1423665v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:55,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:55,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:55,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference/checkm_data
[2024-01-24 13:50:55,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:55,070] [INFO] Task started: CheckM
[2024-01-24 13:50:55,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014236655.1_ASM1423665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014236655.1_ASM1423665v1_genomic.fna/checkm_input GCF_014236655.1_ASM1423665v1_genomic.fna/checkm_result
[2024-01-24 13:51:49,793] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:49,794] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:50,016] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:50,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:50,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014236655.1_ASM1423665v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:50,017] [INFO] Task started: Blastn
[2024-01-24 13:51:50,017] [INFO] Running command: blastn -query GCF_014236655.1_ASM1423665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d90a6f4-72bb-4b33-999e-6b67dd3d2979/dqc_reference/reference_markers_gtdb.fasta -out GCF_014236655.1_ASM1423665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:51,429] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:51,434] [INFO] Selected 25 target genomes.
[2024-01-24 13:51:51,434] [INFO] Target genome list was writen to GCF_014236655.1_ASM1423665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:51,529] [INFO] Task started: fastANI
[2024-01-24 13:51:51,530] [INFO] Running command: fastANI --query /var/lib/cwl/stga273cc6b-2967-4c03-abb3-dd6e90ff170e/GCF_014236655.1_ASM1423665v1_genomic.fna.gz --refList GCF_014236655.1_ASM1423665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014236655.1_ASM1423665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:25,421] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:25,444] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:25,444] [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_014236655.1	s__Pseudomonas_E kielensis	100.0	1957	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.48	99.48	0.90	0.89	3	conclusive
GCF_009834545.1	s__Pseudomonas_E sp900187635	94.3533	1581	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.29	98.57	0.96	0.91	3	-
GCF_900187505.1	s__Pseudomonas_E sp900187505	87.4332	1345	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.03	0.87	0.86	4	-
GCF_900109995.1	s__Pseudomonas_E sp900109995	86.5858	1247	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003732225.1	s__Pseudomonas_E brassicacearum_E	86.321	1252	1961	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_001874645.1	s__Pseudomonas_E frederiksbergensis_B	86.2404	1194	1961	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_000217955.3	s__Pseudomonas_E fluorescens_AQ	86.0956	1231	1961	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_007713465.1	s__Pseudomonas_E sp007713465	86.0576	1215	1961	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_003732665.1	s__Pseudomonas_E frederiksbergensis_G	85.4606	1279	1961	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	85.4429	1280	1961	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_000282415.1	s__Pseudomonas_E sp000282415	85.3708	1257	1961	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_902497855.1	s__Pseudomonas_E fluorescens_BI	85.346	1257	1961	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_000968015.1	s__Pseudomonas_E fluorescens_W	85.327	1251	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_000282315.2	s__Pseudomonas_E sp000282315	85.3216	1266	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.54	96.05	0.87	0.83	6	-
GCF_015461845.1	s__Pseudomonas_E mucoides	85.3199	1309	1961	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_006438925.1	s__Pseudomonas_E mandelii_C	85.275	1257	1961	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_006094435.1	s__Pseudomonas_E sp002029345	85.2749	1296	1961	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_900105495.1	s__Pseudomonas_E frederiksbergensis	85.2501	1283	1961	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_002091715.1	s__Pseudomonas_E migulae	85.2244	1264	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.09	0.95	0.90	3	-
GCF_010095445.1	s__Pseudomonas_E sp010095445	84.6111	1229	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.15	0.85	0.81	4	-
GCF_000783395.1	s__Pseudomonas_E helmanticensis	84.4172	1200	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.23	95.21	0.89	0.89	3	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	84.2552	1176	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_013374995.1	s__Pseudomonas_E eucalypticola	82.0124	928	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	99.03	0.96	0.96	2	-
GCF_017491605.1	s__Pseudomonas sp017491605	80.0769	874	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003488145.1	s__Pseudomonas_A sp003488145	78.4126	357	1961	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.7169	97.61	97.61	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:25,446] [INFO] GTDB search result was written to GCF_014236655.1_ASM1423665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:25,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:25,452] [INFO] DFAST_QC result json was written to GCF_014236655.1_ASM1423665v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:25,453] [INFO] DFAST_QC completed!
[2024-01-24 13:52:25,453] [INFO] Total running time: 0h2m30s