[2023-06-29 20:02:36,897] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:02:36,903] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:02:36,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference
[2023-06-29 20:02:39,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:02:39,820] [INFO] Task started: Prodigal
[2023-06-29 20:02:39,821] [INFO] Running command: gunzip -c /var/lib/cwl/stga1720e52-0950-4796-b119-e93f64235d36/GCA_021827145.1_ASM2182714v1_genomic.fna.gz | prodigal -d GCA_021827145.1_ASM2182714v1_genomic.fna/cds.fna -a GCA_021827145.1_ASM2182714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:02:47,787] [INFO] Task succeeded: Prodigal
[2023-06-29 20:02:47,788] [INFO] Task started: HMMsearch
[2023-06-29 20:02:47,788] [INFO] Running command: hmmsearch --tblout GCA_021827145.1_ASM2182714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference/reference_markers.hmm GCA_021827145.1_ASM2182714v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:02:48,072] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:02:48,074] [INFO] Found 6/6 markers.
[2023-06-29 20:02:48,106] [INFO] Query marker FASTA was written to GCA_021827145.1_ASM2182714v1_genomic.fna/markers.fasta
[2023-06-29 20:02:48,106] [INFO] Task started: Blastn
[2023-06-29 20:02:48,106] [INFO] Running command: blastn -query GCA_021827145.1_ASM2182714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference/reference_markers.fasta -out GCA_021827145.1_ASM2182714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:02:48,942] [INFO] Task succeeded: Blastn
[2023-06-29 20:02:48,946] [INFO] Selected 29 target genomes.
[2023-06-29 20:02:48,947] [INFO] Target genome list was writen to GCA_021827145.1_ASM2182714v1_genomic.fna/target_genomes.txt
[2023-06-29 20:02:48,951] [INFO] Task started: fastANI
[2023-06-29 20:02:48,951] [INFO] Running command: fastANI --query /var/lib/cwl/stga1720e52-0950-4796-b119-e93f64235d36/GCA_021827145.1_ASM2182714v1_genomic.fna.gz --refList GCA_021827145.1_ASM2182714v1_genomic.fna/target_genomes.txt --output GCA_021827145.1_ASM2182714v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:03:04,984] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:04,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:03:04,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:03:04,996] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:03:04,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:03:04,997] [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
Acidiferrobacter thiooxydans	strain=m-1	GCA_003333315.1	163359	163359	type	True	79.3413	423	827	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	76.3876	51	827	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.4982	58	827	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.3304	51	827	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:03:04,999] [INFO] DFAST Taxonomy check result was written to GCA_021827145.1_ASM2182714v1_genomic.fna/tc_result.tsv
[2023-06-29 20:03:05,000] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:03:05,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:03:05,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference/checkm_data
[2023-06-29 20:03:05,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:03:05,040] [INFO] Task started: CheckM
[2023-06-29 20:03:05,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021827145.1_ASM2182714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021827145.1_ASM2182714v1_genomic.fna/checkm_input GCA_021827145.1_ASM2182714v1_genomic.fna/checkm_result
[2023-06-29 20:03:33,066] [INFO] Task succeeded: CheckM
[2023-06-29 20:03:33,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.26%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 20:03:33,090] [INFO] ===== Completeness check finished =====
[2023-06-29 20:03:33,091] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:03:33,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021827145.1_ASM2182714v1_genomic.fna/markers.fasta)
[2023-06-29 20:03:33,092] [INFO] Task started: Blastn
[2023-06-29 20:03:33,092] [INFO] Running command: blastn -query GCA_021827145.1_ASM2182714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacb6e725-8f56-42d2-a9bc-d9cb69f85800/dqc_reference/reference_markers_gtdb.fasta -out GCA_021827145.1_ASM2182714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:03:34,405] [INFO] Task succeeded: Blastn
[2023-06-29 20:03:34,410] [INFO] Selected 28 target genomes.
[2023-06-29 20:03:34,410] [INFO] Target genome list was writen to GCA_021827145.1_ASM2182714v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:03:34,421] [INFO] Task started: fastANI
[2023-06-29 20:03:34,422] [INFO] Running command: fastANI --query /var/lib/cwl/stga1720e52-0950-4796-b119-e93f64235d36/GCA_021827145.1_ASM2182714v1_genomic.fna.gz --refList GCA_021827145.1_ASM2182714v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021827145.1_ASM2182714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:03:49,001] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:49,008] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:03:49,008] [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_003184265.1	s__Acidiferrobacter sp003184265	79.5706	463	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Acidiferrobacteraceae;g__Acidiferrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333315.1	s__Acidiferrobacter thiooxydans	79.3291	425	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Acidiferrobacteraceae;g__Acidiferrobacter	95.0	99.34	99.34	0.91	0.91	2	-
GCA_004298065.1	s__SCRL01 sp004298065	76.5368	55	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__SCRL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355415.1	s__Sulfurifustis variabilis	76.3876	51	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfurifustis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:03:49,011] [INFO] GTDB search result was written to GCA_021827145.1_ASM2182714v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:03:49,011] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:03:49,014] [INFO] DFAST_QC result json was written to GCA_021827145.1_ASM2182714v1_genomic.fna/dqc_result.json
[2023-06-29 20:03:49,014] [INFO] DFAST_QC completed!
[2023-06-29 20:03:49,015] [INFO] Total running time: 0h1m12s