[2023-06-29 13:18:15,563] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:18:15,566] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:18:15,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference
[2023-06-29 13:18:16,795] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:18:16,796] [INFO] Task started: Prodigal
[2023-06-29 13:18:16,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg0948e595-0c48-4f61-9d97-f4470a313ff6/GCA_021821045.1_ASM2182104v1_genomic.fna.gz | prodigal -d GCA_021821045.1_ASM2182104v1_genomic.fna/cds.fna -a GCA_021821045.1_ASM2182104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:18:30,792] [INFO] Task succeeded: Prodigal
[2023-06-29 13:18:30,793] [INFO] Task started: HMMsearch
[2023-06-29 13:18:30,793] [INFO] Running command: hmmsearch --tblout GCA_021821045.1_ASM2182104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference/reference_markers.hmm GCA_021821045.1_ASM2182104v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:18:31,068] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:18:31,069] [INFO] Found 6/6 markers.
[2023-06-29 13:18:31,119] [INFO] Query marker FASTA was written to GCA_021821045.1_ASM2182104v1_genomic.fna/markers.fasta
[2023-06-29 13:18:31,119] [INFO] Task started: Blastn
[2023-06-29 13:18:31,119] [INFO] Running command: blastn -query GCA_021821045.1_ASM2182104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference/reference_markers.fasta -out GCA_021821045.1_ASM2182104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:18:31,911] [INFO] Task succeeded: Blastn
[2023-06-29 13:18:31,915] [INFO] Selected 32 target genomes.
[2023-06-29 13:18:31,915] [INFO] Target genome list was writen to GCA_021821045.1_ASM2182104v1_genomic.fna/target_genomes.txt
[2023-06-29 13:18:31,919] [INFO] Task started: fastANI
[2023-06-29 13:18:31,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg0948e595-0c48-4f61-9d97-f4470a313ff6/GCA_021821045.1_ASM2182104v1_genomic.fna.gz --refList GCA_021821045.1_ASM2182104v1_genomic.fna/target_genomes.txt --output GCA_021821045.1_ASM2182104v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:18:52,246] [INFO] Task succeeded: fastANI
[2023-06-29 13:18:52,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:18:52,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:18:52,265] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:18:52,265] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:18:52,266] [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
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.5947	97	1434	95	below_threshold
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	76.1202	70	1434	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.0795	55	1434	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.0614	90	1434	95	below_threshold
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	75.9445	59	1434	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	75.9076	60	1434	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	75.8748	53	1434	95	below_threshold
Pseudomonas japonica	strain=NBRC 103040	GCA_000730585.1	256466	256466	type	True	75.6452	53	1434	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	75.608	55	1434	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	75.6031	57	1434	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.5405	59	1434	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.5404	69	1434	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	75.5265	73	1434	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.5203	58	1434	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	75.4885	56	1434	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.4505	53	1434	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	75.4425	50	1434	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.41	61	1434	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	75.402	58	1434	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.379	60	1434	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	75.3722	67	1434	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	75.3479	57	1434	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	75.2667	63	1434	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:18:52,268] [INFO] DFAST Taxonomy check result was written to GCA_021821045.1_ASM2182104v1_genomic.fna/tc_result.tsv
[2023-06-29 13:18:52,269] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:18:52,269] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:18:52,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference/checkm_data
[2023-06-29 13:18:52,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:18:52,313] [INFO] Task started: CheckM
[2023-06-29 13:18:52,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021821045.1_ASM2182104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021821045.1_ASM2182104v1_genomic.fna/checkm_input GCA_021821045.1_ASM2182104v1_genomic.fna/checkm_result
[2023-06-29 13:19:35,115] [INFO] Task succeeded: CheckM
[2023-06-29 13:19:35,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:19:35,141] [INFO] ===== Completeness check finished =====
[2023-06-29 13:19:35,142] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:19:35,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021821045.1_ASM2182104v1_genomic.fna/markers.fasta)
[2023-06-29 13:19:35,142] [INFO] Task started: Blastn
[2023-06-29 13:19:35,143] [INFO] Running command: blastn -query GCA_021821045.1_ASM2182104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b278e4-d8ed-4e51-84bd-60915e3b2c40/dqc_reference/reference_markers_gtdb.fasta -out GCA_021821045.1_ASM2182104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:19:36,520] [INFO] Task succeeded: Blastn
[2023-06-29 13:19:36,526] [INFO] Selected 33 target genomes.
[2023-06-29 13:19:36,526] [INFO] Target genome list was writen to GCA_021821045.1_ASM2182104v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:19:36,544] [INFO] Task started: fastANI
[2023-06-29 13:19:36,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg0948e595-0c48-4f61-9d97-f4470a313ff6/GCA_021821045.1_ASM2182104v1_genomic.fna.gz --refList GCA_021821045.1_ASM2182104v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021821045.1_ASM2182104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:19:53,857] [INFO] Task succeeded: fastANI
[2023-06-29 13:19:53,878] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:19:53,878] [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_004001245.1	s__Sulfurivermis fontis	76.5947	97	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.4821	101	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464965.1	s__Ga0077554 sp001464965	76.2742	54	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077554;f__Ga007554;g__Ga0077554	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355735.1	s__Sulfuricaulis limicola	76.0999	71	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	76.0658	67	1434	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_014762505.1	s__SpSt-1174 sp014762505	76.0649	95	1434	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	-
GCA_016218375.1	s__JAHJQQ01 sp016218375	76.0124	72	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011374975.1	s__Thiogranum sp011374975	75.9879	57	1434	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	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	75.9826	61	1434	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_002376325.1	s__Sulfurivermis sp002376325	75.912	68	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012769535.1	s__Methylococcus sp012769535	75.9076	60	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	75.8188	68	1434	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_011051685.1	s__SZUA-152 sp011051685	75.7605	62	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__SZUA-152	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391525.1	s__Competibacter_A sp002391525	75.7423	64	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.79	99.79	0.93	0.93	2	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	75.6601	55	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188455.1	s__Pseudomonas_E japonica	75.5919	56	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	75.475	58	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCF_017589465.1	s__Pseudomonas sp017589465	75.346	72	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013523125.1	s__Pseudomonas_E entomophila_B	75.3238	53	1434	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:19:53,881] [INFO] GTDB search result was written to GCA_021821045.1_ASM2182104v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:19:53,881] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:19:53,886] [INFO] DFAST_QC result json was written to GCA_021821045.1_ASM2182104v1_genomic.fna/dqc_result.json
[2023-06-29 13:19:53,886] [INFO] DFAST_QC completed!
[2023-06-29 13:19:53,886] [INFO] Total running time: 0h1m38s