[2024-01-24 13:37:05,480] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,483] [INFO] DQC Reference Directory: /var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference
[2024-01-24 13:37:06,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,827] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,827] [INFO] Running command: gunzip -c /var/lib/cwl/stgebc3adf5-1bd3-42d2-aa3e-6fc45e6854f8/GCF_000621305.1_ASM62130v1_genomic.fna.gz | prodigal -d GCF_000621305.1_ASM62130v1_genomic.fna/cds.fna -a GCF_000621305.1_ASM62130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:20,730] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:20,731] [INFO] Task started: HMMsearch
[2024-01-24 13:37:20,731] [INFO] Running command: hmmsearch --tblout GCF_000621305.1_ASM62130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference/reference_markers.hmm GCF_000621305.1_ASM62130v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:21,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:21,085] [INFO] Found 6/6 markers.
[2024-01-24 13:37:21,122] [INFO] Query marker FASTA was written to GCF_000621305.1_ASM62130v1_genomic.fna/markers.fasta
[2024-01-24 13:37:21,122] [INFO] Task started: Blastn
[2024-01-24 13:37:21,122] [INFO] Running command: blastn -query GCF_000621305.1_ASM62130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference/reference_markers.fasta -out GCF_000621305.1_ASM62130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:22,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:22,245] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:22,246] [INFO] Target genome list was writen to GCF_000621305.1_ASM62130v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:22,254] [INFO] Task started: fastANI
[2024-01-24 13:37:22,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc3adf5-1bd3-42d2-aa3e-6fc45e6854f8/GCF_000621305.1_ASM62130v1_genomic.fna.gz --refList GCF_000621305.1_ASM62130v1_genomic.fna/target_genomes.txt --output GCF_000621305.1_ASM62130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:34,874] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:34,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:34,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:34,898] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:34,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:34,898] [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
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	100.0	1381	1382	95	conclusive
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	99.9227	1267	1382	95	conclusive
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	88.3822	947	1382	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	84.707	766	1382	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	84.6935	795	1382	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	83.7912	647	1382	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	83.6027	665	1382	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.5008	570	1382	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.8114	535	1382	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.548	496	1382	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.1618	486	1382	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	77.0188	410	1382	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:34,900] [INFO] DFAST Taxonomy check result was written to GCF_000621305.1_ASM62130v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:34,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:34,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:34,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference/checkm_data
[2024-01-24 13:37:34,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:34,945] [INFO] Task started: CheckM
[2024-01-24 13:37:34,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621305.1_ASM62130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621305.1_ASM62130v1_genomic.fna/checkm_input GCF_000621305.1_ASM62130v1_genomic.fna/checkm_result
[2024-01-24 13:38:20,492] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:20,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:20,513] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:20,514] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:20,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621305.1_ASM62130v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:20,515] [INFO] Task started: Blastn
[2024-01-24 13:38:20,515] [INFO] Running command: blastn -query GCF_000621305.1_ASM62130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb682e56f-ec6d-4ace-a8fd-40cbce51e9de/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621305.1_ASM62130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:22,669] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:22,673] [INFO] Selected 12 target genomes.
[2024-01-24 13:38:22,673] [INFO] Target genome list was writen to GCF_000621305.1_ASM62130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:22,690] [INFO] Task started: fastANI
[2024-01-24 13:38:22,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc3adf5-1bd3-42d2-aa3e-6fc45e6854f8/GCF_000621305.1_ASM62130v1_genomic.fna.gz --refList GCF_000621305.1_ASM62130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621305.1_ASM62130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:33,167] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:33,184] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:33,184] [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_000310205.1	s__Thauera linaloolentis	99.9227	1267	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001591165.1	s__Thauera butanivorans	88.3758	947	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245655.1	s__Thauera propionica	84.7205	765	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCF_001051995.2	s__Thauera humireducens	84.673	798	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_000310225.1	s__Thauera phenylacetica	83.7604	650	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	83.6127	664	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_017997795.1	s__Thauera sp017997795	83.473	526	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	83.469	680	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	83.1539	622	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	82.9441	499	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_003030465.1	s__Thauera aromatica	82.7545	604	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	82.4577	711	1382	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:33,186] [INFO] GTDB search result was written to GCF_000621305.1_ASM62130v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:33,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:33,191] [INFO] DFAST_QC result json was written to GCF_000621305.1_ASM62130v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:33,191] [INFO] DFAST_QC completed!
[2024-01-24 13:38:33,192] [INFO] Total running time: 0h1m28s