[2024-01-24 14:14:37,502] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference
[2024-01-24 14:14:39,123] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:39,124] [INFO] Task started: Prodigal
[2024-01-24 14:14:39,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg48a7885b-d9da-4b49-a0e0-824175f740a8/GCF_014284495.1_ASM1428449v1_genomic.fna.gz | prodigal -d GCF_014284495.1_ASM1428449v1_genomic.fna/cds.fna -a GCF_014284495.1_ASM1428449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:49,568] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:49,568] [INFO] Task started: HMMsearch
[2024-01-24 14:14:49,568] [INFO] Running command: hmmsearch --tblout GCF_014284495.1_ASM1428449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference/reference_markers.hmm GCF_014284495.1_ASM1428449v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:49,945] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:49,946] [INFO] Found 6/6 markers.
[2024-01-24 14:14:49,986] [INFO] Query marker FASTA was written to GCF_014284495.1_ASM1428449v1_genomic.fna/markers.fasta
[2024-01-24 14:14:49,986] [INFO] Task started: Blastn
[2024-01-24 14:14:49,986] [INFO] Running command: blastn -query GCF_014284495.1_ASM1428449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference/reference_markers.fasta -out GCF_014284495.1_ASM1428449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:52,793] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:52,797] [INFO] Selected 12 target genomes.
[2024-01-24 14:14:52,797] [INFO] Target genome list was writen to GCF_014284495.1_ASM1428449v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:52,828] [INFO] Task started: fastANI
[2024-01-24 14:14:52,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg48a7885b-d9da-4b49-a0e0-824175f740a8/GCF_014284495.1_ASM1428449v1_genomic.fna.gz --refList GCF_014284495.1_ASM1428449v1_genomic.fna/target_genomes.txt --output GCF_014284495.1_ASM1428449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:02,185] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:02,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:02,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:02,201] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:02,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:02,202] [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
Acetobacterium dehalogenans	strain=DSM 11527	GCA_000472665.1	82116	82116	type	True	96.7433	1087	1326	95	conclusive
Acetobacterium wieringae	strain=DSM 1911	GCA_001766835.1	52694	52694	type	True	84.3467	912	1326	95	below_threshold
Acetobacterium woodii	strain=DSM 1030	GCA_000247605.1	33952	33952	type	True	79.9127	518	1326	95	below_threshold
Acetobacterium bakii	strain=DSM 8239	GCA_008086625.1	52689	52689	type	True	79.2863	361	1326	95	below_threshold
Acetobacterium bakii	strain=DSM 8239	GCA_001263355.1	52689	52689	type	True	79.2265	370	1326	95	below_threshold
Acetobacterium paludosum	strain=DSM 8237	GCA_008086595.1	52693	52693	type	True	78.7827	331	1326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:02,204] [INFO] DFAST Taxonomy check result was written to GCF_014284495.1_ASM1428449v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:02,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:02,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:02,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference/checkm_data
[2024-01-24 14:15:02,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:02,264] [INFO] Task started: CheckM
[2024-01-24 14:15:02,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284495.1_ASM1428449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284495.1_ASM1428449v1_genomic.fna/checkm_input GCF_014284495.1_ASM1428449v1_genomic.fna/checkm_result
[2024-01-24 14:15:40,150] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:40,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,187] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:40,188] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:40,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284495.1_ASM1428449v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:40,189] [INFO] Task started: Blastn
[2024-01-24 14:15:40,189] [INFO] Running command: blastn -query GCF_014284495.1_ASM1428449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb791cf3f-677b-4a07-ad8c-62b3b682848e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284495.1_ASM1428449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:41,695] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:41,700] [INFO] Selected 6 target genomes.
[2024-01-24 14:15:41,700] [INFO] Target genome list was writen to GCF_014284495.1_ASM1428449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:41,705] [INFO] Task started: fastANI
[2024-01-24 14:15:41,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg48a7885b-d9da-4b49-a0e0-824175f740a8/GCF_014284495.1_ASM1428449v1_genomic.fna.gz --refList GCF_014284495.1_ASM1428449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284495.1_ASM1428449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:47,426] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:47,470] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:47,470] [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_000472665.1	s__Acetobacterium dehalogenans	96.7433	1087	1326	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	96.75	96.75	0.83	0.83	2	conclusive
GCA_002841405.1	s__Acetobacterium sp002841405	88.7106	851	1326	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766835.1	s__Acetobacterium wieringae	84.3065	916	1326	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	97.41	97.27	0.88	0.86	5	-
GCF_003260995.1	s__Acetobacterium sp003260995	83.8277	832	1326	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	98.25	98.25	0.82	0.82	2	-
GCA_018903255.1	s__Acetobacterium sp018903255	83.6866	629	1326	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213825.1	s__Acetobacterium woodii_A	82.4919	754	1326	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Eubacteriales;f__Eubacteriaceae;g__Acetobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:47,472] [INFO] GTDB search result was written to GCF_014284495.1_ASM1428449v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:47,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:47,475] [INFO] DFAST_QC result json was written to GCF_014284495.1_ASM1428449v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:47,475] [INFO] DFAST_QC completed!
[2024-01-24 14:15:47,476] [INFO] Total running time: 0h1m10s