[2023-06-29 11:07:33,339] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:07:33,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:07:33,341] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference
[2023-06-29 11:07:35,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:07:35,760] [INFO] Task started: Prodigal
[2023-06-29 11:07:35,761] [INFO] Running command: gunzip -c /var/lib/cwl/stgc07cc832-56da-4b86-99ba-38edb2009fc4/GCA_020847045.1_ASM2084704v1_genomic.fna.gz | prodigal -d GCA_020847045.1_ASM2084704v1_genomic.fna/cds.fna -a GCA_020847045.1_ASM2084704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:07:50,192] [INFO] Task succeeded: Prodigal
[2023-06-29 11:07:50,193] [INFO] Task started: HMMsearch
[2023-06-29 11:07:50,193] [INFO] Running command: hmmsearch --tblout GCA_020847045.1_ASM2084704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference/reference_markers.hmm GCA_020847045.1_ASM2084704v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:07:50,457] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:07:50,459] [INFO] Found 6/6 markers.
[2023-06-29 11:07:50,520] [INFO] Query marker FASTA was written to GCA_020847045.1_ASM2084704v1_genomic.fna/markers.fasta
[2023-06-29 11:07:50,521] [INFO] Task started: Blastn
[2023-06-29 11:07:50,521] [INFO] Running command: blastn -query GCA_020847045.1_ASM2084704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference/reference_markers.fasta -out GCA_020847045.1_ASM2084704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:51,114] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:51,119] [INFO] Selected 32 target genomes.
[2023-06-29 11:07:51,119] [INFO] Target genome list was writen to GCA_020847045.1_ASM2084704v1_genomic.fna/target_genomes.txt
[2023-06-29 11:07:51,136] [INFO] Task started: fastANI
[2023-06-29 11:07:51,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07cc832-56da-4b86-99ba-38edb2009fc4/GCA_020847045.1_ASM2084704v1_genomic.fna.gz --refList GCA_020847045.1_ASM2084704v1_genomic.fna/target_genomes.txt --output GCA_020847045.1_ASM2084704v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:08:13,687] [INFO] Task succeeded: fastANI
[2023-06-29 11:08:13,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:08:13,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:08:13,702] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:08:13,702] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:08:13,702] [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
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.1384	57	1555	95	below_threshold
Paludibaculum fermentans	strain=P105	GCA_015277775.1	1473598	1473598	type	True	76.0991	184	1555	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	75.8205	60	1555	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.4903	53	1555	95	below_threshold
Edaphobacter aggregans	strain=DSM 19364	GCA_000745965.1	570835	570835	type	True	75.2925	59	1555	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	75.0289	57	1555	95	below_threshold
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	75.0252	81	1555	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	75.0252	67	1555	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	74.9985	80	1555	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	74.9064	66	1555	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.9031	67	1555	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	74.8712	60	1555	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	74.8284	64	1555	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:08:13,705] [INFO] DFAST Taxonomy check result was written to GCA_020847045.1_ASM2084704v1_genomic.fna/tc_result.tsv
[2023-06-29 11:08:13,706] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:08:13,706] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:08:13,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference/checkm_data
[2023-06-29 11:08:13,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:08:13,753] [INFO] Task started: CheckM
[2023-06-29 11:08:13,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020847045.1_ASM2084704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020847045.1_ASM2084704v1_genomic.fna/checkm_input GCA_020847045.1_ASM2084704v1_genomic.fna/checkm_result
[2023-06-29 11:08:56,779] [INFO] Task succeeded: CheckM
[2023-06-29 11:08:56,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.93%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 11:08:56,806] [INFO] ===== Completeness check finished =====
[2023-06-29 11:08:56,807] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:08:56,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020847045.1_ASM2084704v1_genomic.fna/markers.fasta)
[2023-06-29 11:08:56,809] [INFO] Task started: Blastn
[2023-06-29 11:08:56,809] [INFO] Running command: blastn -query GCA_020847045.1_ASM2084704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbcd397c-bffd-4a5e-af9c-1164129f8888/dqc_reference/reference_markers_gtdb.fasta -out GCA_020847045.1_ASM2084704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:08:57,645] [INFO] Task succeeded: Blastn
[2023-06-29 11:08:57,651] [INFO] Selected 28 target genomes.
[2023-06-29 11:08:57,651] [INFO] Target genome list was writen to GCA_020847045.1_ASM2084704v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:08:57,655] [INFO] Task started: fastANI
[2023-06-29 11:08:57,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgc07cc832-56da-4b86-99ba-38edb2009fc4/GCA_020847045.1_ASM2084704v1_genomic.fna.gz --refList GCA_020847045.1_ASM2084704v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020847045.1_ASM2084704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:09:22,679] [INFO] Task succeeded: fastANI
[2023-06-29 11:09:22,698] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 11:09:22,699] [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_016713735.1	s__JAFLBB01 sp016713735	79.5075	823	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JAFLBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304135.1	s__JAFLBB01 sp017304135	79.3333	819	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JAFLBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871315.1	s__VFZE01 sp016871315	76.2503	230	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__VFZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871115.1	s__DSOI01 sp016871115	76.2359	199	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__DSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268715.1	s__TMP-7 sp018268715	76.1831	219	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__TMP-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822245.1	s__PNKE01 sp013822245	76.0938	166	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PNKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213755.1	s__JACQZT01 sp016213755	76.084	216	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JACQZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970405.1	s__CAJCIT01 sp903970405	76.0468	59	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CAJCIT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870915.1	s__VFZY01 sp016870915	76.0387	173	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__VFZY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215215.1	s__Paludibaculum sp016215215	76.0217	159	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Paludibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054605.1	s__DSOI01 sp011054605	76.0058	204	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__DSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907865.1	s__BOG-234 sp903907865	75.8702	96	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-234	95.0	99.99	99.99	0.99	0.98	3	-
GCA_019187195.1	s__CADEFT01 sp019187195	75.8581	153	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CADEFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650235.1	s__VFZE01 sp016650235	75.8387	168	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__VFZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178155.1	s__JACMLA01 sp016178155	75.7917	131	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JACMLA01	95.0	99.30	99.30	0.81	0.81	2	-
GCA_016871015.1	s__SYLY01 sp016871015	75.7827	171	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__SYLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178945.1	s__JADJWL01 sp016178945	75.7728	210	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADJWL01	95.0	98.66	98.66	0.85	0.85	2	-
GCA_017883415.1	s__JADGNR01 sp017883415	75.769	156	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADGNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005808475.1	s__SYLY01 sp005808475	75.6026	190	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__SYLY01	95.0	99.92	99.92	0.95	0.95	2	-
GCA_001464575.1	s__Ga0077553 sp001464575	75.5766	118	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Ga0077553	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870995.1	s__Bryobacter sp016870995	75.4846	66	1555	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	74.9459	65	1555	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 11:09:22,701] [INFO] GTDB search result was written to GCA_020847045.1_ASM2084704v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:09:22,701] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:09:22,708] [INFO] DFAST_QC result json was written to GCA_020847045.1_ASM2084704v1_genomic.fna/dqc_result.json
[2023-06-29 11:09:22,708] [INFO] DFAST_QC completed!
[2023-06-29 11:09:22,709] [INFO] Total running time: 0h1m49s