[2024-01-24 12:14:48,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference
[2024-01-24 12:14:50,299] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,300] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg437326fe-43fa-4533-b8b9-d7a90ea89159/GCF_014836765.1_ASM1483676v1_genomic.fna.gz | prodigal -d GCF_014836765.1_ASM1483676v1_genomic.fna/cds.fna -a GCF_014836765.1_ASM1483676v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:03,216] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:03,217] [INFO] Task started: HMMsearch
[2024-01-24 12:15:03,217] [INFO] Running command: hmmsearch --tblout GCF_014836765.1_ASM1483676v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference/reference_markers.hmm GCF_014836765.1_ASM1483676v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:03,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:03,536] [INFO] Found 6/6 markers.
[2024-01-24 12:15:03,591] [INFO] Query marker FASTA was written to GCF_014836765.1_ASM1483676v1_genomic.fna/markers.fasta
[2024-01-24 12:15:03,591] [INFO] Task started: Blastn
[2024-01-24 12:15:03,591] [INFO] Running command: blastn -query GCF_014836765.1_ASM1483676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference/reference_markers.fasta -out GCF_014836765.1_ASM1483676v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,774] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,780] [INFO] Selected 29 target genomes.
[2024-01-24 12:15:04,781] [INFO] Target genome list was writen to GCF_014836765.1_ASM1483676v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:04,793] [INFO] Task started: fastANI
[2024-01-24 12:15:04,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg437326fe-43fa-4533-b8b9-d7a90ea89159/GCF_014836765.1_ASM1483676v1_genomic.fna.gz --refList GCF_014836765.1_ASM1483676v1_genomic.fna/target_genomes.txt --output GCF_014836765.1_ASM1483676v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:30,365] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:30,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:30,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:30,393] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:30,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:30,394] [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
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	100.0	1289	1289	95	conclusive
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	81.6633	766	1289	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	81.6344	778	1289	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.7225	579	1289	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	80.6117	628	1289	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	80.6075	668	1289	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	80.5942	631	1289	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	80.501	597	1289	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	80.4986	608	1289	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	80.4982	623	1289	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	80.4891	604	1289	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	80.4667	605	1289	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	80.4473	589	1289	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	80.4337	588	1289	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	80.3833	671	1289	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	80.3676	689	1289	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	80.2791	674	1289	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	80.2582	653	1289	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	80.2405	669	1289	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	80.1531	641	1289	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	80.1258	642	1289	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	80.103	655	1289	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	80.0261	590	1289	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	80.0135	592	1289	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	79.9728	563	1289	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	79.8554	581	1289	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	79.8469	588	1289	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	79.8076	583	1289	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	79.722	555	1289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:30,395] [INFO] DFAST Taxonomy check result was written to GCF_014836765.1_ASM1483676v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:30,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:30,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:30,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference/checkm_data
[2024-01-24 12:15:30,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:30,436] [INFO] Task started: CheckM
[2024-01-24 12:15:30,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836765.1_ASM1483676v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836765.1_ASM1483676v1_genomic.fna/checkm_input GCF_014836765.1_ASM1483676v1_genomic.fna/checkm_result
[2024-01-24 12:16:08,673] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:08,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:08,699] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:08,700] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:08,700] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836765.1_ASM1483676v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:08,700] [INFO] Task started: Blastn
[2024-01-24 12:16:08,701] [INFO] Running command: blastn -query GCF_014836765.1_ASM1483676v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5587ce41-3acc-4883-b8d1-6753ee87b737/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836765.1_ASM1483676v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:10,661] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:10,666] [INFO] Selected 25 target genomes.
[2024-01-24 12:16:10,666] [INFO] Target genome list was writen to GCF_014836765.1_ASM1483676v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:10,684] [INFO] Task started: fastANI
[2024-01-24 12:16:10,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg437326fe-43fa-4533-b8b9-d7a90ea89159/GCF_014836765.1_ASM1483676v1_genomic.fna.gz --refList GCF_014836765.1_ASM1483676v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836765.1_ASM1483676v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:33,059] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:33,083] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:33,083] [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
GCA_014836765.1	s__Pseudomonas_H sp014836765	100.0	1289	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	97.71	97.71	0.94	0.94	2	conclusive
GCF_000802425.1	s__Pseudomonas_H flexibilis	81.6656	775	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	99.07	98.74	0.94	0.90	5	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	80.7965	625	1289	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_000263395.1	s__Pseudomonas_A stutzeri_C	80.7411	598	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	80.6288	636	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000467105.1	s__Pseudomonas_E alcaligenes	80.5992	629	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_005508865.1	s__Pseudomonas_E sp005508865	80.5928	601	1289	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_003696305.1	s__Pseudomonas_E sp003696305	80.5907	675	1289	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	80.5874	671	1289	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_015070855.1	s__Pseudomonas_A lopnurensis	80.5723	621	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_003696285.1	s__Pseudomonas_A nitrititolerans	80.5012	602	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.45	96.83	0.90	0.83	53	-
GCF_005844005.1	s__Pseudomonas_A sp000765155	80.3749	602	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.19	98.01	0.92	0.89	5	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	80.2965	596	1289	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_000016565.1	s__Pseudomonas_E mendocina_A	80.2817	705	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_012767755.2	s__Pseudomonas_F sp003234055	80.2677	652	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	80.2225	571	1289	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_001839655.1	s__Pseudomonas_E argentinensis_B	80.2187	594	1289	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_000412695.1	s__Pseudomonas_F resinovorans_A	80.0651	647	1289	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_000219605.1	s__Pseudomonas_A stutzeri	80.0436	587	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	79.8641	580	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	79.8483	602	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	79.7649	648	1289	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_014700075.1	s__Pseudomonas_F sp014700075	79.7585	605	1289	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_000935215.1	s__Pseudomonas_A stutzeri_AD	79.6586	561	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCA_002339675.1	s__Pseudomonas_A stutzeri_O	79.6367	542	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:33,086] [INFO] GTDB search result was written to GCF_014836765.1_ASM1483676v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:33,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:33,093] [INFO] DFAST_QC result json was written to GCF_014836765.1_ASM1483676v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:33,094] [INFO] DFAST_QC completed!
[2024-01-24 12:16:33,094] [INFO] Total running time: 0h1m44s