[2024-01-24 11:51:37,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,085] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference
[2024-01-24 11:51:38,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,373] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c504233-fd69-49e1-9f0a-49f90bd04fa4/GCF_021556395.1_ASM2155639v1_genomic.fna.gz | prodigal -d GCF_021556395.1_ASM2155639v1_genomic.fna/cds.fna -a GCF_021556395.1_ASM2155639v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:53,899] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:53,900] [INFO] Task started: HMMsearch
[2024-01-24 11:51:53,900] [INFO] Running command: hmmsearch --tblout GCF_021556395.1_ASM2155639v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference/reference_markers.hmm GCF_021556395.1_ASM2155639v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:54,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:54,214] [INFO] Found 6/6 markers.
[2024-01-24 11:51:54,262] [INFO] Query marker FASTA was written to GCF_021556395.1_ASM2155639v1_genomic.fna/markers.fasta
[2024-01-24 11:51:54,263] [INFO] Task started: Blastn
[2024-01-24 11:51:54,263] [INFO] Running command: blastn -query GCF_021556395.1_ASM2155639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference/reference_markers.fasta -out GCF_021556395.1_ASM2155639v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:55,103] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:55,108] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:55,109] [INFO] Target genome list was writen to GCF_021556395.1_ASM2155639v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:55,116] [INFO] Task started: fastANI
[2024-01-24 11:51:55,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c504233-fd69-49e1-9f0a-49f90bd04fa4/GCF_021556395.1_ASM2155639v1_genomic.fna.gz --refList GCF_021556395.1_ASM2155639v1_genomic.fna/target_genomes.txt --output GCF_021556395.1_ASM2155639v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:08,822] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:08,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:08,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:08,840] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:08,840] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:08,840] [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
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	83.0785	1212	1848	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	79.7814	813	1848	95	below_threshold
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	78.943	832	1848	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	78.843	653	1848	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	78.8277	651	1848	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.6834	208	1848	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	76.3868	297	1848	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	76.331	217	1848	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	76.222	265	1848	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	76.1792	214	1848	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	75.7957	188	1848	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.764	118	1848	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.6738	184	1848	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	75.6527	152	1848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:08,850] [INFO] DFAST Taxonomy check result was written to GCF_021556395.1_ASM2155639v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:08,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:08,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:08,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference/checkm_data
[2024-01-24 11:52:08,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:08,907] [INFO] Task started: CheckM
[2024-01-24 11:52:08,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021556395.1_ASM2155639v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021556395.1_ASM2155639v1_genomic.fna/checkm_input GCF_021556395.1_ASM2155639v1_genomic.fna/checkm_result
[2024-01-24 11:52:57,036] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:57,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:57,058] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:57,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:57,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021556395.1_ASM2155639v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:57,059] [INFO] Task started: Blastn
[2024-01-24 11:52:57,060] [INFO] Running command: blastn -query GCF_021556395.1_ASM2155639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59255199-f063-4cb2-9957-f7f057cb4753/dqc_reference/reference_markers_gtdb.fasta -out GCF_021556395.1_ASM2155639v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,422] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,426] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:58,426] [INFO] Target genome list was writen to GCF_021556395.1_ASM2155639v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:58,442] [INFO] Task started: fastANI
[2024-01-24 11:52:58,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c504233-fd69-49e1-9f0a-49f90bd04fa4/GCF_021556395.1_ASM2155639v1_genomic.fna.gz --refList GCF_021556395.1_ASM2155639v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021556395.1_ASM2155639v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:13,528] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:13,544] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:13,544] [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_016411865.1	s__Acuticoccus sp016411865	79.814	808	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258595.1	s__Acuticoccus sediminis	78.9841	821	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927245.1	s__Acuticoccus yangtzensis	78.8172	652	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	98.76	97.53	0.97	0.95	3	-
GCF_014050225.1	s__Hongsoonwoonella albiluteola	76.9826	235	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374525.1	s__Amorphus coralli	76.9609	331	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789575.1	s__Stappia indica_A	76.9535	335	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009600605.1	s__Pseudoxanthobacter spirostomi	76.8758	394	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	76.7308	392	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839445.1	s__Chthonobacter albigriseus	76.7247	279	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	76.7036	348	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_015482775.1	s__Kaustia mangrovi	76.374	299	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.2296	429	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000022085.1	s__Methylobacterium nodulans	76.1591	322	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975005.1	s__17J80-11 sp010975005	75.8554	158	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__17J80-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	75.6501	186	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696345.1	s__Roseomonas sp003696345	75.6459	153	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_014380005.1	s__Magnetospirillum sp014380005	75.4456	67	1848	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:13,546] [INFO] GTDB search result was written to GCF_021556395.1_ASM2155639v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:13,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:13,550] [INFO] DFAST_QC result json was written to GCF_021556395.1_ASM2155639v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:13,550] [INFO] DFAST_QC completed!
[2024-01-24 11:53:13,550] [INFO] Total running time: 0h1m36s