[2023-06-29 08:44:46,479] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:44:46,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:44:46,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference
[2023-06-29 08:44:47,796] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:44:47,797] [INFO] Task started: Prodigal
[2023-06-29 08:44:47,797] [INFO] Running command: gunzip -c /var/lib/cwl/stg83e68e2d-5610-4f01-a7c8-bf72b716fab3/GCA_020852575.1_ASM2085257v1_genomic.fna.gz | prodigal -d GCA_020852575.1_ASM2085257v1_genomic.fna/cds.fna -a GCA_020852575.1_ASM2085257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:44:53,470] [INFO] Task succeeded: Prodigal
[2023-06-29 08:44:53,471] [INFO] Task started: HMMsearch
[2023-06-29 08:44:53,471] [INFO] Running command: hmmsearch --tblout GCA_020852575.1_ASM2085257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference/reference_markers.hmm GCA_020852575.1_ASM2085257v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:44:53,707] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:44:53,708] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg83e68e2d-5610-4f01-a7c8-bf72b716fab3/GCA_020852575.1_ASM2085257v1_genomic.fna.gz]
[2023-06-29 08:44:53,736] [INFO] Query marker FASTA was written to GCA_020852575.1_ASM2085257v1_genomic.fna/markers.fasta
[2023-06-29 08:44:53,736] [INFO] Task started: Blastn
[2023-06-29 08:44:53,737] [INFO] Running command: blastn -query GCA_020852575.1_ASM2085257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference/reference_markers.fasta -out GCA_020852575.1_ASM2085257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:44:54,475] [INFO] Task succeeded: Blastn
[2023-06-29 08:44:54,480] [INFO] Selected 23 target genomes.
[2023-06-29 08:44:54,480] [INFO] Target genome list was writen to GCA_020852575.1_ASM2085257v1_genomic.fna/target_genomes.txt
[2023-06-29 08:44:54,490] [INFO] Task started: fastANI
[2023-06-29 08:44:54,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e68e2d-5610-4f01-a7c8-bf72b716fab3/GCA_020852575.1_ASM2085257v1_genomic.fna.gz --refList GCA_020852575.1_ASM2085257v1_genomic.fna/target_genomes.txt --output GCA_020852575.1_ASM2085257v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:45:10,479] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:10,480] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:45:10,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:45:10,505] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:45:10,505] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:45:10,506] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	80.1423	299	578	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	80.084	297	578	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.8317	254	578	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.8313	260	578	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	78.7468	233	578	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	78.7111	232	578	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	78.7093	238	578	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	78.4946	298	578	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.4792	211	578	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.4439	270	578	95	below_threshold
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	78.2922	237	578	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.1506	221	578	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.1252	219	578	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.0859	241	578	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	77.9112	194	578	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.5956	189	578	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1848	180	578	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.085	181	578	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	76.5622	131	578	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	76.4129	101	578	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	76.2344	92	578	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.9456	116	578	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	75.9189	80	578	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:45:10,508] [INFO] DFAST Taxonomy check result was written to GCA_020852575.1_ASM2085257v1_genomic.fna/tc_result.tsv
[2023-06-29 08:45:10,509] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:45:10,509] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:45:10,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference/checkm_data
[2023-06-29 08:45:10,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:45:10,540] [INFO] Task started: CheckM
[2023-06-29 08:45:10,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020852575.1_ASM2085257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020852575.1_ASM2085257v1_genomic.fna/checkm_input GCA_020852575.1_ASM2085257v1_genomic.fna/checkm_result
[2023-06-29 08:45:32,678] [INFO] Task succeeded: CheckM
[2023-06-29 08:45:32,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:45:32,700] [INFO] ===== Completeness check finished =====
[2023-06-29 08:45:32,700] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:45:32,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020852575.1_ASM2085257v1_genomic.fna/markers.fasta)
[2023-06-29 08:45:32,701] [INFO] Task started: Blastn
[2023-06-29 08:45:32,701] [INFO] Running command: blastn -query GCA_020852575.1_ASM2085257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ed97e18-2081-4910-80c9-0de2591ae203/dqc_reference/reference_markers_gtdb.fasta -out GCA_020852575.1_ASM2085257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:45:33,779] [INFO] Task succeeded: Blastn
[2023-06-29 08:45:33,784] [INFO] Selected 9 target genomes.
[2023-06-29 08:45:33,784] [INFO] Target genome list was writen to GCA_020852575.1_ASM2085257v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:45:33,812] [INFO] Task started: fastANI
[2023-06-29 08:45:33,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e68e2d-5610-4f01-a7c8-bf72b716fab3/GCA_020852575.1_ASM2085257v1_genomic.fna.gz --refList GCA_020852575.1_ASM2085257v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020852575.1_ASM2085257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:45:39,321] [INFO] Task succeeded: fastANI
[2023-06-29 08:45:39,333] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 08:45:39,333] [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_011526165.1	s__Desulfobacillus sp011526165	98.7023	496	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.84	98.84	0.79	0.79	2	conclusive
GCA_008933825.1	s__Desulfobacillus sp008933825	89.8873	412	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCA_003105015.1	s__Desulfobacillus sp003105015	88.2211	492	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.07	97.07	0.88	0.88	2	-
GCA_017347485.1	s__Desulfobacillus denitrificans	88.0024	455	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	98.90	98.32	0.92	0.90	5	-
GCA_016868295.1	s__Desulfobacillus sp016868295	86.6862	409	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791205.1	s__Desulfobacillus sp016791205	86.6635	386	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214145.1	s__Desulfobacillus sp016214145	86.5807	459	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339315.1	s__Desulfobacillus sp905339315	86.3614	334	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.66	96.66	0.91	0.89	3	-
GCA_016880375.1	s__Desulfobacillus sp016880375	85.1073	286	578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:45:39,336] [INFO] GTDB search result was written to GCA_020852575.1_ASM2085257v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:45:39,337] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:45:39,341] [INFO] DFAST_QC result json was written to GCA_020852575.1_ASM2085257v1_genomic.fna/dqc_result.json
[2023-06-29 08:45:39,342] [INFO] DFAST_QC completed!
[2023-06-29 08:45:39,342] [INFO] Total running time: 0h0m53s