[2024-01-25 18:02:20,610] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:20,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:20,611] [INFO] DQC Reference Directory: /var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference
[2024-01-25 18:02:21,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:21,707] [INFO] Task started: Prodigal
[2024-01-25 18:02:21,707] [INFO] Running command: gunzip -c /var/lib/cwl/stgda2f66f6-69ff-4c1d-afdf-ceded79849f5/GCF_000188175.1_ASM18817v1_genomic.fna.gz | prodigal -d GCF_000188175.1_ASM18817v1_genomic.fna/cds.fna -a GCF_000188175.1_ASM18817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:26,141] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:26,141] [INFO] Task started: HMMsearch
[2024-01-25 18:02:26,141] [INFO] Running command: hmmsearch --tblout GCF_000188175.1_ASM18817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference/reference_markers.hmm GCF_000188175.1_ASM18817v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:26,344] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:26,345] [INFO] Found 6/6 markers.
[2024-01-25 18:02:26,366] [INFO] Query marker FASTA was written to GCF_000188175.1_ASM18817v1_genomic.fna/markers.fasta
[2024-01-25 18:02:26,366] [INFO] Task started: Blastn
[2024-01-25 18:02:26,366] [INFO] Running command: blastn -query GCF_000188175.1_ASM18817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference/reference_markers.fasta -out GCF_000188175.1_ASM18817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:26,913] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:26,917] [INFO] Selected 18 target genomes.
[2024-01-25 18:02:26,918] [INFO] Target genome list was writen to GCF_000188175.1_ASM18817v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:26,964] [INFO] Task started: fastANI
[2024-01-25 18:02:26,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2f66f6-69ff-4c1d-afdf-ceded79849f5/GCF_000188175.1_ASM18817v1_genomic.fna.gz --refList GCF_000188175.1_ASM18817v1_genomic.fna/target_genomes.txt --output GCF_000188175.1_ASM18817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:38,027] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:38,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:38,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:38,031] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:38,031] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:38,031] [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
Phascolarctobacterium succinatutens	strain=YIT 12067	GCA_000188175.1	626940	626940	type	True	100.0	657	664	95	conclusive
Phascolarctobacterium faecium	strain=DSM 14760	GCA_003269275.1	33025	33025	type	True	77.4221	104	664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:38,033] [INFO] DFAST Taxonomy check result was written to GCF_000188175.1_ASM18817v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:38,033] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:38,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:38,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference/checkm_data
[2024-01-25 18:02:38,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:38,058] [INFO] Task started: CheckM
[2024-01-25 18:02:38,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000188175.1_ASM18817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000188175.1_ASM18817v1_genomic.fna/checkm_input GCF_000188175.1_ASM18817v1_genomic.fna/checkm_result
[2024-01-25 18:02:56,468] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:56,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:56,488] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:56,488] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:56,488] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000188175.1_ASM18817v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:56,488] [INFO] Task started: Blastn
[2024-01-25 18:02:56,489] [INFO] Running command: blastn -query GCF_000188175.1_ASM18817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafe32203-2df8-48cf-80ab-55af762a29d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000188175.1_ASM18817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:57,260] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:57,262] [INFO] Selected 7 target genomes.
[2024-01-25 18:02:57,262] [INFO] Target genome list was writen to GCF_000188175.1_ASM18817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:57,269] [INFO] Task started: fastANI
[2024-01-25 18:02:57,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2f66f6-69ff-4c1d-afdf-ceded79849f5/GCF_000188175.1_ASM18817v1_genomic.fna.gz --refList GCF_000188175.1_ASM18817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000188175.1_ASM18817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:00,618] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:00,623] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:00,624] [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_000188175.1	s__Phascolarctobacterium_A succinatutens	100.0	657	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	97.32	95.06	0.90	0.84	17	conclusive
GCA_900753045.1	s__Phascolarctobacterium_A sp900753045	94.8821	562	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434895.1	s__Phascolarctobacterium_A succinatutens_A	94.4356	571	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	95.38	95.36	0.85	0.80	4	-
GCA_900770955.1	s__Phascolarctobacterium_A sp900770955	92.7542	565	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551335.1	s__Phascolarctobacterium_A sp900551335	82.2033	283	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	96.01	95.96	0.95	0.94	3	-
GCA_905212365.1	s__Phascolarctobacterium_A sp905212365	79.1409	286	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553055.1	s__Phascolarctobacterium_A sp900553055	78.7415	185	664	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	98.03	96.65	0.77	0.68	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:00,625] [INFO] GTDB search result was written to GCF_000188175.1_ASM18817v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:00,625] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:00,627] [INFO] DFAST_QC result json was written to GCF_000188175.1_ASM18817v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:00,627] [INFO] DFAST_QC completed!
[2024-01-25 18:03:00,627] [INFO] Total running time: 0h0m40s