[2024-01-24 14:30:29,844] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:29,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:29,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference
[2024-01-24 14:30:31,231] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,233] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,233] [INFO] Running command: gunzip -c /var/lib/cwl/stgca0fca53-cd9b-47ce-b545-40e9de22ed06/GCF_902859615.1_LMG_6003_genomic.fna.gz | prodigal -d GCF_902859615.1_LMG_6003_genomic.fna/cds.fna -a GCF_902859615.1_LMG_6003_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:52,180] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:52,180] [INFO] Task started: HMMsearch
[2024-01-24 14:30:52,180] [INFO] Running command: hmmsearch --tblout GCF_902859615.1_LMG_6003_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference/reference_markers.hmm GCF_902859615.1_LMG_6003_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:52,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:52,506] [INFO] Found 6/6 markers.
[2024-01-24 14:30:52,569] [INFO] Query marker FASTA was written to GCF_902859615.1_LMG_6003_genomic.fna/markers.fasta
[2024-01-24 14:30:52,570] [INFO] Task started: Blastn
[2024-01-24 14:30:52,570] [INFO] Running command: blastn -query GCF_902859615.1_LMG_6003_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference/reference_markers.fasta -out GCF_902859615.1_LMG_6003_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:53,612] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:53,615] [INFO] Selected 9 target genomes.
[2024-01-24 14:30:53,615] [INFO] Target genome list was writen to GCF_902859615.1_LMG_6003_genomic.fna/target_genomes.txt
[2024-01-24 14:30:53,625] [INFO] Task started: fastANI
[2024-01-24 14:30:53,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0fca53-cd9b-47ce-b545-40e9de22ed06/GCF_902859615.1_LMG_6003_genomic.fna.gz --refList GCF_902859615.1_LMG_6003_genomic.fna/target_genomes.txt --output GCF_902859615.1_LMG_6003_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:06,987] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:06,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:06,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:06,997] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:31:06,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:06,997] [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
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	100.0	2122	2125	95	conclusive
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	99.999	2124	2125	95	conclusive
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	99.9905	2120	2125	95	conclusive
Achromobacter insolitus	strain=DSM 23807	GCA_001971645.1	217204	217204	type	True	99.9876	2125	2125	95	conclusive
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	98.9845	2035	2125	95	conclusive
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.2226	1441	2125	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.9015	854	2125	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7254	313	2125	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.0236	272	2125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:06,999] [INFO] DFAST Taxonomy check result was written to GCF_902859615.1_LMG_6003_genomic.fna/tc_result.tsv
[2024-01-24 14:31:07,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:07,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:07,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference/checkm_data
[2024-01-24 14:31:07,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:07,060] [INFO] Task started: CheckM
[2024-01-24 14:31:07,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859615.1_LMG_6003_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859615.1_LMG_6003_genomic.fna/checkm_input GCF_902859615.1_LMG_6003_genomic.fna/checkm_result
[2024-01-24 14:32:06,938] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:06,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:06,957] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:06,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:06,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859615.1_LMG_6003_genomic.fna/markers.fasta)
[2024-01-24 14:32:06,957] [INFO] Task started: Blastn
[2024-01-24 14:32:06,958] [INFO] Running command: blastn -query GCF_902859615.1_LMG_6003_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b5c05db-f71b-4c89-a5f3-bb15581eae67/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859615.1_LMG_6003_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:08,900] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:08,903] [INFO] Selected 7 target genomes.
[2024-01-24 14:32:08,903] [INFO] Target genome list was writen to GCF_902859615.1_LMG_6003_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:08,909] [INFO] Task started: fastANI
[2024-01-24 14:32:08,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgca0fca53-cd9b-47ce-b545-40e9de22ed06/GCF_902859615.1_LMG_6003_genomic.fna.gz --refList GCF_902859615.1_LMG_6003_genomic.fna/target_genomes_gtdb.txt --output GCF_902859615.1_LMG_6003_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:21,255] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:21,262] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:21,262] [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_002209555.1	s__Achromobacter insolitus	99.9905	2120	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.13	98.86	0.96	0.89	17	conclusive
GCF_002192695.1	s__Achromobacter xylosoxidans_C	90.0521	1822	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_014490035.1	s__Achromobacter bronchisepticus_A	89.9544	1822	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_902859735.1	s__Achromobacter aegrifaciens	89.8833	1834	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	89.8408	1840	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_903652925.1	s__Achromobacter anxifer	89.3617	1776	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	-
GCF_002885955.2	s__Achromobacter pulmonis_A	86.3185	1459	2125	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:21,264] [INFO] GTDB search result was written to GCF_902859615.1_LMG_6003_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:21,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:21,268] [INFO] DFAST_QC result json was written to GCF_902859615.1_LMG_6003_genomic.fna/dqc_result.json
[2024-01-24 14:32:21,268] [INFO] DFAST_QC completed!
[2024-01-24 14:32:21,268] [INFO] Total running time: 0h1m51s