[2024-01-24 11:43:25,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference
[2024-01-24 11:43:30,055] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,056] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg489157e0-f629-4bdd-80b5-2fb010de5259/GCF_003104955.1_ASM310495v1_genomic.fna.gz | prodigal -d GCF_003104955.1_ASM310495v1_genomic.fna/cds.fna -a GCF_003104955.1_ASM310495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,607] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,607] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,608] [INFO] Running command: hmmsearch --tblout GCF_003104955.1_ASM310495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference/reference_markers.hmm GCF_003104955.1_ASM310495v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:54,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:54,962] [INFO] Found 6/6 markers.
[2024-01-24 11:43:55,030] [INFO] Query marker FASTA was written to GCF_003104955.1_ASM310495v1_genomic.fna/markers.fasta
[2024-01-24 11:43:55,030] [INFO] Task started: Blastn
[2024-01-24 11:43:55,031] [INFO] Running command: blastn -query GCF_003104955.1_ASM310495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference/reference_markers.fasta -out GCF_003104955.1_ASM310495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:55,930] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:55,934] [INFO] Selected 9 target genomes.
[2024-01-24 11:43:55,934] [INFO] Target genome list was writen to GCF_003104955.1_ASM310495v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:55,938] [INFO] Task started: fastANI
[2024-01-24 11:43:55,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg489157e0-f629-4bdd-80b5-2fb010de5259/GCF_003104955.1_ASM310495v1_genomic.fna.gz --refList GCF_003104955.1_ASM310495v1_genomic.fna/target_genomes.txt --output GCF_003104955.1_ASM310495v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:08,912] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:08,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:08,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:08,926] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:08,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:08,926] [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
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	100.0	2571	2583	95	conclusive
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	86.1038	1788	2583	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	85.659	1718	2583	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	84.8349	1638	2583	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	82.2747	1312	2583	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0312	116	2583	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.8891	125	2583	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.837	122	2583	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.7184	120	2583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:08,928] [INFO] DFAST Taxonomy check result was written to GCF_003104955.1_ASM310495v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:08,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:08,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:08,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference/checkm_data
[2024-01-24 11:44:08,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:09,006] [INFO] Task started: CheckM
[2024-01-24 11:44:09,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003104955.1_ASM310495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003104955.1_ASM310495v1_genomic.fna/checkm_input GCF_003104955.1_ASM310495v1_genomic.fna/checkm_result
[2024-01-24 11:45:20,418] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:20,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:20,443] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:20,443] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:20,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003104955.1_ASM310495v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:20,444] [INFO] Task started: Blastn
[2024-01-24 11:45:20,444] [INFO] Running command: blastn -query GCF_003104955.1_ASM310495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg034841cf-e268-42ff-8cda-a27ffb82b6f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003104955.1_ASM310495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:22,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:22,099] [INFO] Selected 5 target genomes.
[2024-01-24 11:45:22,100] [INFO] Target genome list was writen to GCF_003104955.1_ASM310495v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:22,105] [INFO] Task started: fastANI
[2024-01-24 11:45:22,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg489157e0-f629-4bdd-80b5-2fb010de5259/GCF_003104955.1_ASM310495v1_genomic.fna.gz --refList GCF_003104955.1_ASM310495v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003104955.1_ASM310495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:31,094] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:31,104] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:45:31,104] [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_009932555.1	s__Steroidobacter_A agaridevorans	86.098	1789	2583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	99.33	99.33	0.96	0.96	2	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	85.6564	1718	2583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138485.1	s__Steroidobacter_A soli	84.8437	1636	2583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801985.1	s__Steroidobacter_A sp016801985	82.2846	1310	2583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790065.1	s__Steroidobacter_A sp016790065	82.2186	1095	2583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:31,105] [INFO] GTDB search result was written to GCF_003104955.1_ASM310495v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:31,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:31,109] [INFO] DFAST_QC result json was written to GCF_003104955.1_ASM310495v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:31,109] [INFO] DFAST_QC completed!
[2024-01-24 11:45:31,109] [INFO] Total running time: 0h2m6s