[2024-01-24 13:40:30,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,240] [INFO] DQC Reference Directory: /var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference
[2024-01-24 13:40:31,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,527] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,528] [INFO] Running command: gunzip -c /var/lib/cwl/stgc71f3a14-f162-447d-98b8-7df6e8cea74f/GCF_000425045.1_ASM42504v1_genomic.fna.gz | prodigal -d GCF_000425045.1_ASM42504v1_genomic.fna/cds.fna -a GCF_000425045.1_ASM42504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:38,251] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:38,252] [INFO] Task started: HMMsearch
[2024-01-24 13:40:38,252] [INFO] Running command: hmmsearch --tblout GCF_000425045.1_ASM42504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference/reference_markers.hmm GCF_000425045.1_ASM42504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:38,503] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:38,504] [INFO] Found 6/6 markers.
[2024-01-24 13:40:38,530] [INFO] Query marker FASTA was written to GCF_000425045.1_ASM42504v1_genomic.fna/markers.fasta
[2024-01-24 13:40:38,530] [INFO] Task started: Blastn
[2024-01-24 13:40:38,530] [INFO] Running command: blastn -query GCF_000425045.1_ASM42504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference/reference_markers.fasta -out GCF_000425045.1_ASM42504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:39,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:39,132] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:39,132] [INFO] Target genome list was writen to GCF_000425045.1_ASM42504v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:39,143] [INFO] Task started: fastANI
[2024-01-24 13:40:39,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgc71f3a14-f162-447d-98b8-7df6e8cea74f/GCF_000425045.1_ASM42504v1_genomic.fna.gz --refList GCF_000425045.1_ASM42504v1_genomic.fna/target_genomes.txt --output GCF_000425045.1_ASM42504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:46,043] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:46,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:46,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:46,050] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:46,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:46,050] [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
Acidaminococcus intestini	strain=DSM 21505	GCA_000425045.1	187327	187327	type	True	99.9995	730	732	95	conclusive
Acidaminococcus provencensis	strain=Marseille-P4266	GCA_900291475.1	2058289	2058289	type	True	78.2812	128	732	95	below_threshold
Acidaminococcus fermentans	strain=DSM 20731	GCA_000025305.1	905	905	type	True	78.209	137	732	95	below_threshold
Acidaminococcus massiliensis	strain=Marseille-P2828	GCA_900095825.1	1852375	1852375	type	True	78.1264	136	732	95	below_threshold
Acidaminococcus timonensis	strain=Marseille-P2764	GCA_900106585.1	1871002	1871002	type	True	77.9718	127	732	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:46,052] [INFO] DFAST Taxonomy check result was written to GCF_000425045.1_ASM42504v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:46,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:46,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:46,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference/checkm_data
[2024-01-24 13:40:46,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:46,081] [INFO] Task started: CheckM
[2024-01-24 13:40:46,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000425045.1_ASM42504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000425045.1_ASM42504v1_genomic.fna/checkm_input GCF_000425045.1_ASM42504v1_genomic.fna/checkm_result
[2024-01-24 13:41:11,875] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:11,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:11,894] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:11,894] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:11,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000425045.1_ASM42504v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:11,895] [INFO] Task started: Blastn
[2024-01-24 13:41:11,895] [INFO] Running command: blastn -query GCF_000425045.1_ASM42504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ef7732-2e89-4afa-8ea4-79a639736e54/dqc_reference/reference_markers_gtdb.fasta -out GCF_000425045.1_ASM42504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:12,754] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:12,757] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:12,757] [INFO] Target genome list was writen to GCF_000425045.1_ASM42504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:12,773] [INFO] Task started: fastANI
[2024-01-24 13:41:12,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgc71f3a14-f162-447d-98b8-7df6e8cea74f/GCF_000425045.1_ASM42504v1_genomic.fna.gz --refList GCF_000425045.1_ASM42504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000425045.1_ASM42504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:19,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,147] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:19,148] [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_000425045.1	s__Acidaminococcus intestini	99.9995	730	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.60	99.25	0.93	0.88	13	conclusive
GCA_900538365.1	s__Acidaminococcus sp900538365	92.1361	590	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.99	97.67	0.93	0.89	4	-
GCF_009696675.1	s__Acidaminococcus sp000437815	78.3693	130	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.16	97.76	0.92	0.89	4	-
GCF_000025305.1	s__Acidaminococcus fermentans	78.2076	137	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.69	98.27	0.92	0.87	11	-
GCF_900095825.1	s__Acidaminococcus massiliensis	78.1317	137	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.55	97.11	0.93	0.86	3	-
GCA_902796945.1	s__Acidaminococcus sp902796945	78.0128	208	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770265.1	s__Acidaminococcus sp900770265	77.9934	92	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	96.61	96.61	0.81	0.81	2	-
GCA_900315205.1	s__Acidaminococcus sp900315205	77.9333	171	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.22	98.84	0.89	0.88	6	-
GCA_905215645.1	s__Acidaminococcus sp905215645	77.609	125	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314165.1	s__Acidaminococcus sp900314165	77.2424	103	732	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,150] [INFO] GTDB search result was written to GCF_000425045.1_ASM42504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:19,150] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:19,153] [INFO] DFAST_QC result json was written to GCF_000425045.1_ASM42504v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:19,154] [INFO] DFAST_QC completed!
[2024-01-24 13:41:19,154] [INFO] Total running time: 0h0m49s