[2024-01-24 13:49:19,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,456] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference
[2024-01-24 13:49:20,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,907] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg28abf4cb-b176-4191-8bfa-67507141e720/GCF_001051995.2_ASM105199v2_genomic.fna.gz | prodigal -d GCF_001051995.2_ASM105199v2_genomic.fna/cds.fna -a GCF_001051995.2_ASM105199v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,528] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,528] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,528] [INFO] Running command: hmmsearch --tblout GCF_001051995.2_ASM105199v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference/reference_markers.hmm GCF_001051995.2_ASM105199v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,848] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,850] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,892] [INFO] Query marker FASTA was written to GCF_001051995.2_ASM105199v2_genomic.fna/markers.fasta
[2024-01-24 13:49:34,892] [INFO] Task started: Blastn
[2024-01-24 13:49:34,893] [INFO] Running command: blastn -query GCF_001051995.2_ASM105199v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference/reference_markers.fasta -out GCF_001051995.2_ASM105199v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:36,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:36,025] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:36,025] [INFO] Target genome list was writen to GCF_001051995.2_ASM105199v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:36,030] [INFO] Task started: fastANI
[2024-01-24 13:49:36,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg28abf4cb-b176-4191-8bfa-67507141e720/GCF_001051995.2_ASM105199v2_genomic.fna.gz --refList GCF_001051995.2_ASM105199v2_genomic.fna/target_genomes.txt --output GCF_001051995.2_ASM105199v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:49,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:49,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:49,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:49,131] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:49,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:49,131] [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 humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	100.0	1388	1390	95	conclusive
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	91.6659	1035	1390	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	85.0154	820	1390	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	84.8354	713	1390	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	84.7344	752	1390	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	84.6926	807	1390	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	84.509	769	1390	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.8394	630	1390	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	80.0597	573	1390	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.7074	543	1390	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.6588	514	1390	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.4938	388	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,133] [INFO] DFAST Taxonomy check result was written to GCF_001051995.2_ASM105199v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:49,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:49,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:49,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference/checkm_data
[2024-01-24 13:49:49,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:49,191] [INFO] Task started: CheckM
[2024-01-24 13:49:49,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001051995.2_ASM105199v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001051995.2_ASM105199v2_genomic.fna/checkm_input GCF_001051995.2_ASM105199v2_genomic.fna/checkm_result
[2024-01-24 13:50:43,251] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:43,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:43,272] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:43,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:43,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001051995.2_ASM105199v2_genomic.fna/markers.fasta)
[2024-01-24 13:50:43,273] [INFO] Task started: Blastn
[2024-01-24 13:50:43,273] [INFO] Running command: blastn -query GCF_001051995.2_ASM105199v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ecec45d-f65c-445e-b435-3b2f58046de1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001051995.2_ASM105199v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:45,432] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:45,435] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:45,435] [INFO] Target genome list was writen to GCF_001051995.2_ASM105199v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:45,450] [INFO] Task started: fastANI
[2024-01-24 13:50:45,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg28abf4cb-b176-4191-8bfa-67507141e720/GCF_001051995.2_ASM105199v2_genomic.fna.gz --refList GCF_001051995.2_ASM105199v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001051995.2_ASM105199v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:56,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:56,594] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:56,595] [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_001051995.2	s__Thauera humireducens	100.0	1388	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	conclusive
GCF_002245655.1	s__Thauera propionica	91.6659	1035	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.06	98.06	0.86	0.86	2	-
GCF_001591165.1	s__Thauera butanivorans	85.0054	821	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	84.8852	710	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310205.1	s__Thauera linaloolentis	84.7481	751	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017997795.1	s__Thauera sp017997795	84.6569	562	1390	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	84.5611	763	1390	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	84.5067	769	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_002422685.1	s__Thauera sp002422685	84.148	688	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310145.2	s__Thauera sp000310145	83.9418	831	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.71	98.54	0.88	0.86	4	-
GCF_001922305.1	s__Thauera chlorobenzoica	83.7756	693	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCA_018240785.1	s__Thauera sp018240785	83.447	778	1390	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 13:50:56,602] [INFO] GTDB search result was written to GCF_001051995.2_ASM105199v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:56,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:56,607] [INFO] DFAST_QC result json was written to GCF_001051995.2_ASM105199v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:56,607] [INFO] DFAST_QC completed!
[2024-01-24 13:50:56,607] [INFO] Total running time: 0h1m37s