[2023-06-29 14:58:55,930] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:58:55,932] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:58:55,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference
[2023-06-29 14:58:58,851] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:58:58,852] [INFO] Task started: Prodigal
[2023-06-29 14:58:58,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e804bb3-28bb-4351-b39d-6cdfc92907ea/GCA_021299035.1_ASM2129903v1_genomic.fna.gz | prodigal -d GCA_021299035.1_ASM2129903v1_genomic.fna/cds.fna -a GCA_021299035.1_ASM2129903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:59:06,302] [INFO] Task succeeded: Prodigal
[2023-06-29 14:59:06,302] [INFO] Task started: HMMsearch
[2023-06-29 14:59:06,303] [INFO] Running command: hmmsearch --tblout GCA_021299035.1_ASM2129903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference/reference_markers.hmm GCA_021299035.1_ASM2129903v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:59:06,545] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:59:06,547] [INFO] Found 6/6 markers.
[2023-06-29 14:59:06,576] [INFO] Query marker FASTA was written to GCA_021299035.1_ASM2129903v1_genomic.fna/markers.fasta
[2023-06-29 14:59:06,576] [INFO] Task started: Blastn
[2023-06-29 14:59:06,576] [INFO] Running command: blastn -query GCA_021299035.1_ASM2129903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference/reference_markers.fasta -out GCA_021299035.1_ASM2129903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:59:07,344] [INFO] Task succeeded: Blastn
[2023-06-29 14:59:07,349] [INFO] Selected 26 target genomes.
[2023-06-29 14:59:07,349] [INFO] Target genome list was writen to GCA_021299035.1_ASM2129903v1_genomic.fna/target_genomes.txt
[2023-06-29 14:59:07,380] [INFO] Task started: fastANI
[2023-06-29 14:59:07,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e804bb3-28bb-4351-b39d-6cdfc92907ea/GCA_021299035.1_ASM2129903v1_genomic.fna.gz --refList GCA_021299035.1_ASM2129903v1_genomic.fna/target_genomes.txt --output GCA_021299035.1_ASM2129903v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:59:27,683] [INFO] Task succeeded: fastANI
[2023-06-29 14:59:27,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:59:27,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:59:27,711] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:59:27,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:59:27,711] [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
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	76.8922	115	819	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	76.8215	117	819	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	76.818	108	819	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.8167	113	819	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	76.7744	106	819	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	76.7266	97	819	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	76.7197	94	819	95	below_threshold
Collimonas arenae	strain=Ter10	GCA_001584165.1	279058	279058	type	True	76.712	95	819	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.693	97	819	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	76.6814	106	819	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	76.6578	145	819	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	76.6232	91	819	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	76.5296	101	819	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	76.5244	107	819	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	76.4948	95	819	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.4849	100	819	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	76.4472	93	819	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	76.4454	82	819	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.3893	96	819	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	76.3859	77	819	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	76.3698	107	819	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	76.3602	89	819	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	76.3073	81	819	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	76.298	98	819	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	76.2246	102	819	95	below_threshold
Duganella sacchari	strain=Sac-22	GCA_900143065.1	551987	551987	type	True	76.1387	99	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:59:27,714] [INFO] DFAST Taxonomy check result was written to GCA_021299035.1_ASM2129903v1_genomic.fna/tc_result.tsv
[2023-06-29 14:59:27,715] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:59:27,715] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:59:27,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference/checkm_data
[2023-06-29 14:59:27,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:59:27,745] [INFO] Task started: CheckM
[2023-06-29 14:59:27,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021299035.1_ASM2129903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021299035.1_ASM2129903v1_genomic.fna/checkm_input GCA_021299035.1_ASM2129903v1_genomic.fna/checkm_result
[2023-06-29 14:59:55,135] [INFO] Task succeeded: CheckM
[2023-06-29 14:59:55,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:59:55,159] [INFO] ===== Completeness check finished =====
[2023-06-29 14:59:55,159] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:59:55,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021299035.1_ASM2129903v1_genomic.fna/markers.fasta)
[2023-06-29 14:59:55,160] [INFO] Task started: Blastn
[2023-06-29 14:59:55,160] [INFO] Running command: blastn -query GCA_021299035.1_ASM2129903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83db13e1-4e65-4582-b335-a194ba6a8216/dqc_reference/reference_markers_gtdb.fasta -out GCA_021299035.1_ASM2129903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:59:56,455] [INFO] Task succeeded: Blastn
[2023-06-29 14:59:56,460] [INFO] Selected 24 target genomes.
[2023-06-29 14:59:56,460] [INFO] Target genome list was writen to GCA_021299035.1_ASM2129903v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:59:56,464] [INFO] Task started: fastANI
[2023-06-29 14:59:56,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e804bb3-28bb-4351-b39d-6cdfc92907ea/GCA_021299035.1_ASM2129903v1_genomic.fna.gz --refList GCA_021299035.1_ASM2129903v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021299035.1_ASM2129903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:00:12,532] [INFO] Task succeeded: fastANI
[2023-06-29 15:00:12,554] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:00:12,554] [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_018882935.1	s__SYFN01 sp018882935	80.7575	480	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	98.35	98.35	0.89	0.89	2	-
GCA_016868055.1	s__SYFN01 sp016868055	80.6983	451	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024875.1	s__SYFN01 sp010024875	77.2409	197	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342585.1	s__Paucimonas lemoignei	77.0791	95	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016467405.1	s__Lacisediminimonas sp016467405	76.9753	108	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299005.1	s__SYFN01 sp900299005	76.9741	154	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	99.47	99.47	0.89	0.89	2	-
GCF_004114795.1	s__Paucimonas sp004114795	76.9513	91	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577615.1	s__Herbaspirillum sp000577615	76.8631	102	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635065.1	s__Oxalicibacterium flavum	76.8385	107	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282135.1	s__Herbaspirillum sp000282135	76.794	95	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	76.7703	100	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590835.1	s__Paucimonas sp003590835	76.7546	120	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241865.1	s__Paucimonas sp018241865	76.7389	77	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719195.1	s__Herbaspirillum rubrisubalbicans	76.7266	97	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.49	96.58	0.87	0.83	8	-
GCF_900188095.1	s__Noviherbaspirillum humi	76.7012	105	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016632335.1	s__Noviherbaspirillum_A pedocola	76.6721	144	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004134995.1	s__Herbaspirillum sp004134995	76.6438	82	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189915.1	s__Herbaspirillum autotrophicum	76.5703	99	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636315.1	s__Undibacterium terreum	76.556	67	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852535.1	s__Herminiimonas sp003852535	76.534	84	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192645.1	s__Herbaspirillum sp014192645	76.5192	68	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_010365165.1	s__CAILRJ01 sp010365165	76.4782	82	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601275.1	s__Janthinobacterium lividum_E	76.4553	74	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	96.41	96.40	0.93	0.92	4	-
GCA_003133225.1	s__Janthinobacterium sp003133225	76.4424	62	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:00:12,557] [INFO] GTDB search result was written to GCA_021299035.1_ASM2129903v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:00:12,557] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:00:12,563] [INFO] DFAST_QC result json was written to GCA_021299035.1_ASM2129903v1_genomic.fna/dqc_result.json
[2023-06-29 15:00:12,563] [INFO] DFAST_QC completed!
[2023-06-29 15:00:12,563] [INFO] Total running time: 0h1m17s