[2024-01-24 12:21:44,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference
[2024-01-24 12:21:46,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:46,085] [INFO] Task started: Prodigal
[2024-01-24 12:21:46,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg14ef37c3-097f-43a6-bc79-eb7f7f61720d/GCF_004340685.1_ASM434068v1_genomic.fna.gz | prodigal -d GCF_004340685.1_ASM434068v1_genomic.fna/cds.fna -a GCF_004340685.1_ASM434068v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:02,000] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:02,001] [INFO] Task started: HMMsearch
[2024-01-24 12:22:02,001] [INFO] Running command: hmmsearch --tblout GCF_004340685.1_ASM434068v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference/reference_markers.hmm GCF_004340685.1_ASM434068v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:02,456] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:02,458] [INFO] Found 6/6 markers.
[2024-01-24 12:22:02,514] [INFO] Query marker FASTA was written to GCF_004340685.1_ASM434068v1_genomic.fna/markers.fasta
[2024-01-24 12:22:02,515] [INFO] Task started: Blastn
[2024-01-24 12:22:02,515] [INFO] Running command: blastn -query GCF_004340685.1_ASM434068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference/reference_markers.fasta -out GCF_004340685.1_ASM434068v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:03,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:03,173] [INFO] Selected 26 target genomes.
[2024-01-24 12:22:03,173] [INFO] Target genome list was writen to GCF_004340685.1_ASM434068v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:03,186] [INFO] Task started: fastANI
[2024-01-24 12:22:03,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg14ef37c3-097f-43a6-bc79-eb7f7f61720d/GCF_004340685.1_ASM434068v1_genomic.fna.gz --refList GCF_004340685.1_ASM434068v1_genomic.fna/target_genomes.txt --output GCF_004340685.1_ASM434068v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:21,517] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:21,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:21,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:21,522] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:21,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:21,523] [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
Hydrogenispora ethanolica	strain=LX-B	GCA_004340685.1	1082276	1082276	type	True	100.0	1941	1946	95	conclusive
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.7079	51	1946	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:21,525] [INFO] DFAST Taxonomy check result was written to GCF_004340685.1_ASM434068v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:21,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:21,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:21,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference/checkm_data
[2024-01-24 12:22:21,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:21,589] [INFO] Task started: CheckM
[2024-01-24 12:22:21,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340685.1_ASM434068v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340685.1_ASM434068v1_genomic.fna/checkm_input GCF_004340685.1_ASM434068v1_genomic.fna/checkm_result
[2024-01-24 12:23:10,206] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:10,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:10,237] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:10,237] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:10,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340685.1_ASM434068v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:10,238] [INFO] Task started: Blastn
[2024-01-24 12:23:10,238] [INFO] Running command: blastn -query GCF_004340685.1_ASM434068v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3162aed7-e2aa-44da-9a3c-0526249bd15a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340685.1_ASM434068v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:11,170] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:11,175] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:11,175] [INFO] Target genome list was writen to GCF_004340685.1_ASM434068v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:11,196] [INFO] Task started: fastANI
[2024-01-24 12:23:11,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg14ef37c3-097f-43a6-bc79-eb7f7f61720d/GCF_004340685.1_ASM434068v1_genomic.fna.gz --refList GCF_004340685.1_ASM434068v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340685.1_ASM434068v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:25,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:25,601] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:25,601] [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_004340685.1	s__Hydrogenispora ethanolica	100.0	1941	1946	d__Bacteria;p__Firmicutes_G;c__UBA4882;o__UBA8346;f__UBA8346;g__Hydrogenispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003501365.1	s__UBA8346 sp003501365	76.87	60	1946	d__Bacteria;p__Firmicutes_G;c__UBA4882;o__UBA8346;f__UBA8346;g__UBA8346	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012735315.1	s__JAAYHS01 sp012735315	76.153	65	1946	d__Bacteria;p__Firmicutes_G;c__UBA4882;o__UBA8346;f__UBA8346;g__JAAYHS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,602] [INFO] GTDB search result was written to GCF_004340685.1_ASM434068v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:25,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:25,605] [INFO] DFAST_QC result json was written to GCF_004340685.1_ASM434068v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:25,606] [INFO] DFAST_QC completed!
[2024-01-24 12:23:25,606] [INFO] Total running time: 0h1m41s