[2023-06-29 20:06:21,370] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:06:21,372] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:06:21,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference
[2023-06-29 20:06:22,783] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:06:22,786] [INFO] Task started: Prodigal
[2023-06-29 20:06:22,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d6ae47d-7410-41e3-a4bc-3532f86bfe3c/GCA_011774445.1_ASM1177444v1_genomic.fna.gz | prodigal -d GCA_011774445.1_ASM1177444v1_genomic.fna/cds.fna -a GCA_011774445.1_ASM1177444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:06:34,648] [INFO] Task succeeded: Prodigal
[2023-06-29 20:06:34,648] [INFO] Task started: HMMsearch
[2023-06-29 20:06:34,648] [INFO] Running command: hmmsearch --tblout GCA_011774445.1_ASM1177444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference/reference_markers.hmm GCA_011774445.1_ASM1177444v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:06:34,972] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:06:34,973] [INFO] Found 6/6 markers.
[2023-06-29 20:06:35,024] [INFO] Query marker FASTA was written to GCA_011774445.1_ASM1177444v1_genomic.fna/markers.fasta
[2023-06-29 20:06:35,024] [INFO] Task started: Blastn
[2023-06-29 20:06:35,024] [INFO] Running command: blastn -query GCA_011774445.1_ASM1177444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference/reference_markers.fasta -out GCA_011774445.1_ASM1177444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:06:36,019] [INFO] Task succeeded: Blastn
[2023-06-29 20:06:36,023] [INFO] Selected 32 target genomes.
[2023-06-29 20:06:36,024] [INFO] Target genome list was writen to GCA_011774445.1_ASM1177444v1_genomic.fna/target_genomes.txt
[2023-06-29 20:06:36,025] [INFO] Task started: fastANI
[2023-06-29 20:06:36,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d6ae47d-7410-41e3-a4bc-3532f86bfe3c/GCA_011774445.1_ASM1177444v1_genomic.fna.gz --refList GCA_011774445.1_ASM1177444v1_genomic.fna/target_genomes.txt --output GCA_011774445.1_ASM1177444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:06:57,351] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:57,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:06:57,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:06:57,381] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:06:57,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:06:57,382] [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
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5516	164	1278	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.4862	200	1278	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.4552	83	1278	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.406	114	1278	95	below_threshold
Halorhodospira halophila	strain=SL1	GCA_000015585.1	1053	1053	suspected-type	True	76.3576	88	1278	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.3518	75	1278	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.3302	102	1278	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.2825	112	1278	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.2707	84	1278	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.0949	114	1278	95	below_threshold
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	76.0837	116	1278	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.0358	109	1278	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.9923	90	1278	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.9875	204	1278	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	75.9178	99	1278	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.8669	145	1278	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.8638	154	1278	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	75.7862	110	1278	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	75.7121	93	1278	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	75.6995	80	1278	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.6657	120	1278	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	75.626	135	1278	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	75.6195	88	1278	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	75.6195	88	1278	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	75.6164	121	1278	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	75.5285	105	1278	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.4876	64	1278	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	75.4562	66	1278	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.4348	65	1278	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	75.2482	92	1278	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	75.1706	129	1278	95	below_threshold
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	75.0546	50	1278	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:06:57,384] [INFO] DFAST Taxonomy check result was written to GCA_011774445.1_ASM1177444v1_genomic.fna/tc_result.tsv
[2023-06-29 20:06:57,385] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:06:57,385] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:06:57,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference/checkm_data
[2023-06-29 20:06:57,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:06:57,426] [INFO] Task started: CheckM
[2023-06-29 20:06:57,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011774445.1_ASM1177444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011774445.1_ASM1177444v1_genomic.fna/checkm_input GCA_011774445.1_ASM1177444v1_genomic.fna/checkm_result
[2023-06-29 20:07:33,538] [INFO] Task succeeded: CheckM
[2023-06-29 20:07:33,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:07:33,564] [INFO] ===== Completeness check finished =====
[2023-06-29 20:07:33,564] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:07:33,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011774445.1_ASM1177444v1_genomic.fna/markers.fasta)
[2023-06-29 20:07:33,565] [INFO] Task started: Blastn
[2023-06-29 20:07:33,565] [INFO] Running command: blastn -query GCA_011774445.1_ASM1177444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb37faba1-b15a-4e4a-b772-b65d518e2c55/dqc_reference/reference_markers_gtdb.fasta -out GCA_011774445.1_ASM1177444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:07:35,340] [INFO] Task succeeded: Blastn
[2023-06-29 20:07:35,345] [INFO] Selected 21 target genomes.
[2023-06-29 20:07:35,345] [INFO] Target genome list was writen to GCA_011774445.1_ASM1177444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:07:35,351] [INFO] Task started: fastANI
[2023-06-29 20:07:35,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d6ae47d-7410-41e3-a4bc-3532f86bfe3c/GCA_011774445.1_ASM1177444v1_genomic.fna.gz --refList GCA_011774445.1_ASM1177444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011774445.1_ASM1177444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:07:48,487] [INFO] Task succeeded: fastANI
[2023-06-29 20:07:48,507] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:07:48,507] [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_011775625.1	s__JAABYT01 sp011775625	100.0	992	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__HK1;f__HK1;g__JAABYT01	95.0	99.82	99.55	0.93	0.76	18	conclusive
GCA_009937425.1	s__JAABYT01 sp009937425	78.3265	567	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__HK1;f__HK1;g__JAABYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	76.6334	77	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.607	100	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.5623	163	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.4603	110	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	76.4552	83	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494165.1	s__S144-34 sp015494165	76.3597	146	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.3338	92	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937385.1	s__QNFN01 sp009937385	76.2135	131	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__QNFN01;f__QNFN01;g__QNFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018409545.1	s__Allochromatium tepidum	76.0514	108	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	75.9976	81	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	75.9706	206	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	75.8801	152	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.8273	158	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	75.7121	143	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	75.6507	85	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	75.6231	82	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	75.5717	146	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903914615.1	s__Rubrivivax sp903914615	75.2945	109	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790515.1	s__Aquabacterium_A sp016790515	75.257	145	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:07:48,510] [INFO] GTDB search result was written to GCA_011774445.1_ASM1177444v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:07:48,510] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:07:48,515] [INFO] DFAST_QC result json was written to GCA_011774445.1_ASM1177444v1_genomic.fna/dqc_result.json
[2023-06-29 20:07:48,516] [INFO] DFAST_QC completed!
[2023-06-29 20:07:48,516] [INFO] Total running time: 0h1m27s