[2024-01-24 13:57:41,925] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,927] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference
[2024-01-24 13:57:43,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,362] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,362] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c13eb04-ae9c-4e7a-abe6-c0a81055325b/GCF_006503695.1_ASM650369v1_genomic.fna.gz | prodigal -d GCF_006503695.1_ASM650369v1_genomic.fna/cds.fna -a GCF_006503695.1_ASM650369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:50,662] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:50,662] [INFO] Task started: HMMsearch
[2024-01-24 13:57:50,662] [INFO] Running command: hmmsearch --tblout GCF_006503695.1_ASM650369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference/reference_markers.hmm GCF_006503695.1_ASM650369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:50,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:50,918] [INFO] Found 6/6 markers.
[2024-01-24 13:57:50,956] [INFO] Query marker FASTA was written to GCF_006503695.1_ASM650369v1_genomic.fna/markers.fasta
[2024-01-24 13:57:50,956] [INFO] Task started: Blastn
[2024-01-24 13:57:50,956] [INFO] Running command: blastn -query GCF_006503695.1_ASM650369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference/reference_markers.fasta -out GCF_006503695.1_ASM650369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:51,880] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:51,883] [INFO] Selected 6 target genomes.
[2024-01-24 13:57:51,884] [INFO] Target genome list was writen to GCF_006503695.1_ASM650369v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:51,887] [INFO] Task started: fastANI
[2024-01-24 13:57:51,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c13eb04-ae9c-4e7a-abe6-c0a81055325b/GCF_006503695.1_ASM650369v1_genomic.fna.gz --refList GCF_006503695.1_ASM650369v1_genomic.fna/target_genomes.txt --output GCF_006503695.1_ASM650369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:55,584] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:55,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:55,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:55,592] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:55,592] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:55,592] [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
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001418245.1	876478	876478	suspected-type	True	98.7545	704	771	95	conclusive
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001517365.1	876478	876478	suspected-type	True	98.7294	705	771	95	conclusive
Tepidiphilus margaritifer	strain=DSM 15129	GCA_000425565.1	203471	203471	type	True	91.4584	624	771	95	below_threshold
Tepidiphilus baoligensis	strain=B18-69	GCA_012911495.1	2698687	2698687	type	True	89.9276	584	771	95	below_threshold
Tepidiphilus olei	strain=J18	GCA_006980705.1	2502184	2502184	type	True	89.2918	598	771	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	78.1144	302	771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:55,594] [INFO] DFAST Taxonomy check result was written to GCF_006503695.1_ASM650369v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:55,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:55,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:55,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference/checkm_data
[2024-01-24 13:57:55,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:55,621] [INFO] Task started: CheckM
[2024-01-24 13:57:55,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006503695.1_ASM650369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006503695.1_ASM650369v1_genomic.fna/checkm_input GCF_006503695.1_ASM650369v1_genomic.fna/checkm_result
[2024-01-24 13:58:23,551] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:23,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,572] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:23,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:23,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006503695.1_ASM650369v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:23,573] [INFO] Task started: Blastn
[2024-01-24 13:58:23,574] [INFO] Running command: blastn -query GCF_006503695.1_ASM650369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7410b4a5-24b2-442f-b3b2-3e562ec9961f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006503695.1_ASM650369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:25,306] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:25,310] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:25,310] [INFO] Target genome list was writen to GCF_006503695.1_ASM650369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:25,323] [INFO] Task started: fastANI
[2024-01-24 13:58:25,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c13eb04-ae9c-4e7a-abe6-c0a81055325b/GCF_006503695.1_ASM650369v1_genomic.fna.gz --refList GCF_006503695.1_ASM650369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006503695.1_ASM650369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:31,694] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:31,703] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:31,704] [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_006503695.1	s__Tepidiphilus succinatimandens	100.0	771	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	98.86	98.78	0.95	0.95	4	conclusive
GCA_016235745.1	s__Tepidiphilus sp016235745	91.7477	553	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425565.1	s__Tepidiphilus margaritifer	91.4584	624	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911495.1	s__Tepidiphilus baoligensis	89.9531	583	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	97.01	96.91	0.89	0.87	3	-
GCA_003963015.1	s__Thauera sp003963015	78.2159	296	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	78.1869	280	771	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	78.0876	305	771	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	77.9185	254	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724315.1	s__SCN-69-89 sp001724315	76.7462	122	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.3151	151	771	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:31,705] [INFO] GTDB search result was written to GCF_006503695.1_ASM650369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:31,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:31,710] [INFO] DFAST_QC result json was written to GCF_006503695.1_ASM650369v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:31,710] [INFO] DFAST_QC completed!
[2024-01-24 13:58:31,710] [INFO] Total running time: 0h0m50s