[2024-01-24 12:47:05,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,183] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference
[2024-01-24 12:47:06,446] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,447] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,447] [INFO] Running command: gunzip -c /var/lib/cwl/stg3812e83b-6e55-4ebb-8459-67eb813c096b/GCF_003550015.1_ASM355001v1_genomic.fna.gz | prodigal -d GCF_003550015.1_ASM355001v1_genomic.fna/cds.fna -a GCF_003550015.1_ASM355001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:09,753] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:09,754] [INFO] Task started: HMMsearch
[2024-01-24 12:47:09,754] [INFO] Running command: hmmsearch --tblout GCF_003550015.1_ASM355001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference/reference_markers.hmm GCF_003550015.1_ASM355001v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:09,998] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:09,999] [INFO] Found 6/6 markers.
[2024-01-24 12:47:10,024] [INFO] Query marker FASTA was written to GCF_003550015.1_ASM355001v1_genomic.fna/markers.fasta
[2024-01-24 12:47:10,024] [INFO] Task started: Blastn
[2024-01-24 12:47:10,025] [INFO] Running command: blastn -query GCF_003550015.1_ASM355001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference/reference_markers.fasta -out GCF_003550015.1_ASM355001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:10,597] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:10,601] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:10,602] [INFO] Target genome list was writen to GCF_003550015.1_ASM355001v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:10,627] [INFO] Task started: fastANI
[2024-01-24 12:47:10,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg3812e83b-6e55-4ebb-8459-67eb813c096b/GCF_003550015.1_ASM355001v1_genomic.fna.gz --refList GCF_003550015.1_ASM355001v1_genomic.fna/target_genomes.txt --output GCF_003550015.1_ASM355001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:20,186] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:20,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:20,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:20,194] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:20,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:20,194] [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
Anaeroplasma bactoclasticum	strain=ATCC 27112	GCA_003550015.1	2088	2088	type	True	100.0	699	702	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:47:20,197] [INFO] DFAST Taxonomy check result was written to GCF_003550015.1_ASM355001v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:20,198] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:20,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:20,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference/checkm_data
[2024-01-24 12:47:20,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:20,228] [INFO] Task started: CheckM
[2024-01-24 12:47:20,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003550015.1_ASM355001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003550015.1_ASM355001v1_genomic.fna/checkm_input GCF_003550015.1_ASM355001v1_genomic.fna/checkm_result
[2024-01-24 12:47:38,121] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:38,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:38,155] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:38,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:38,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003550015.1_ASM355001v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:38,156] [INFO] Task started: Blastn
[2024-01-24 12:47:38,156] [INFO] Running command: blastn -query GCF_003550015.1_ASM355001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc0db6c1-8d36-4fe1-88a4-e0923365feb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003550015.1_ASM355001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:38,951] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:38,956] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:38,956] [INFO] Target genome list was writen to GCF_003550015.1_ASM355001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:38,988] [INFO] Task started: fastANI
[2024-01-24 12:47:38,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg3812e83b-6e55-4ebb-8459-67eb813c096b/GCF_003550015.1_ASM355001v1_genomic.fna.gz --refList GCF_003550015.1_ASM355001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003550015.1_ASM355001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:45,327] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:45,339] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:45,340] [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_003550015.1	s__Anaeroplasma bactoclasticum	100.0	699	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017388605.1	s__Anaeroplasma sp017388605	84.1947	350	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	98.33	98.33	0.79	0.79	2	-
GCA_002449755.1	s__Anaeroplasma sp002449755	78.5574	168	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	98.36	98.36	0.87	0.87	2	-
GCA_017441525.1	s__Anaeroplasma sp017441525	78.3215	149	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016280975.1	s__Anaeroplasma sp016280975	78.2858	140	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	96.20	96.20	0.69	0.69	2	-
GCA_017449215.1	s__Anaeroplasma sp017449215	78.2501	197	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	95.35	95.35	0.87	0.87	2	-
GCA_017462645.1	s__Anaeroplasma sp017462645	78.1295	84	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017524905.1	s__Anaeroplasma sp017524905	77.8508	155	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288855.1	s__Anaeroplasma sp016288855	77.6871	148	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900767915.1	s__Anaeroplasma sp900767915	77.5627	116	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059145.1	s__Anaeroplasma sp015059145	77.5001	117	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783745.1	s__Anaeroplasma sp902783745	77.4176	96	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715825.1	s__Anaeroplasma faecigallinarum	77.0899	51	702	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:45,341] [INFO] GTDB search result was written to GCF_003550015.1_ASM355001v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:45,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:45,344] [INFO] DFAST_QC result json was written to GCF_003550015.1_ASM355001v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:45,345] [INFO] DFAST_QC completed!
[2024-01-24 12:47:45,345] [INFO] Total running time: 0h0m40s