[2023-06-04 18:00:15,752] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:00:15,756] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:00:15,756] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference
[2023-06-04 18:00:17,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:00:17,158] [INFO] Task started: Prodigal
[2023-06-04 18:00:17,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg53b5eef7-bdbd-4d61-a4e5-ecc3068aa1b3/GCA_004554325.1_ASM455432v1_genomic.fna.gz | prodigal -d GCA_004554325.1_ASM455432v1_genomic.fna/cds.fna -a GCA_004554325.1_ASM455432v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:00:20,360] [INFO] Task succeeded: Prodigal
[2023-06-04 18:00:20,360] [INFO] Task started: HMMsearch
[2023-06-04 18:00:20,360] [INFO] Running command: hmmsearch --tblout GCA_004554325.1_ASM455432v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference/reference_markers.hmm GCA_004554325.1_ASM455432v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:00:20,576] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:00:20,577] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg53b5eef7-bdbd-4d61-a4e5-ecc3068aa1b3/GCA_004554325.1_ASM455432v1_genomic.fna.gz]
[2023-06-04 18:00:20,599] [INFO] Query marker FASTA was written to GCA_004554325.1_ASM455432v1_genomic.fna/markers.fasta
[2023-06-04 18:00:20,599] [INFO] Task started: Blastn
[2023-06-04 18:00:20,600] [INFO] Running command: blastn -query GCA_004554325.1_ASM455432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference/reference_markers.fasta -out GCA_004554325.1_ASM455432v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:21,132] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:21,140] [INFO] Selected 11 target genomes.
[2023-06-04 18:00:21,141] [INFO] Target genome list was writen to GCA_004554325.1_ASM455432v1_genomic.fna/target_genomes.txt
[2023-06-04 18:00:21,185] [INFO] Task started: fastANI
[2023-06-04 18:00:21,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b5eef7-bdbd-4d61-a4e5-ecc3068aa1b3/GCA_004554325.1_ASM455432v1_genomic.fna.gz --refList GCA_004554325.1_ASM455432v1_genomic.fna/target_genomes.txt --output GCA_004554325.1_ASM455432v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:00:27,053] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:27,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:00:27,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:00:27,060] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:00:27,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:00:27,061] [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	79.2196	151	312	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:00:27,064] [INFO] DFAST Taxonomy check result was written to GCA_004554325.1_ASM455432v1_genomic.fna/tc_result.tsv
[2023-06-04 18:00:27,064] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:00:27,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:00:27,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference/checkm_data
[2023-06-04 18:00:27,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:00:27,087] [INFO] Task started: CheckM
[2023-06-04 18:00:27,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004554325.1_ASM455432v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004554325.1_ASM455432v1_genomic.fna/checkm_input GCA_004554325.1_ASM455432v1_genomic.fna/checkm_result
[2023-06-04 18:00:44,497] [INFO] Task succeeded: CheckM
[2023-06-04 18:00:44,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:00:44,522] [INFO] ===== Completeness check finished =====
[2023-06-04 18:00:44,523] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:00:44,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004554325.1_ASM455432v1_genomic.fna/markers.fasta)
[2023-06-04 18:00:44,523] [INFO] Task started: Blastn
[2023-06-04 18:00:44,524] [INFO] Running command: blastn -query GCA_004554325.1_ASM455432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf34f7ec-5a24-4936-bffa-9233a2047471/dqc_reference/reference_markers_gtdb.fasta -out GCA_004554325.1_ASM455432v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:00:45,147] [INFO] Task succeeded: Blastn
[2023-06-04 18:00:45,152] [INFO] Selected 10 target genomes.
[2023-06-04 18:00:45,152] [INFO] Target genome list was writen to GCA_004554325.1_ASM455432v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:00:45,304] [INFO] Task started: fastANI
[2023-06-04 18:00:45,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg53b5eef7-bdbd-4d61-a4e5-ecc3068aa1b3/GCA_004554325.1_ASM455432v1_genomic.fna.gz --refList GCA_004554325.1_ASM455432v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004554325.1_ASM455432v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:00:48,707] [INFO] Task succeeded: fastANI
[2023-06-04 18:00:48,721] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:00:48,722] [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
GCA_900553055.1	s__Phascolarctobacterium_A sp900553055	96.6504	212	312	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	conclusive
GCA_004562175.1	s__Phascolarctobacterium_A sp004562175	84.6262	164	312	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_004558595.1	s__Phascolarctobacterium_A sp004558595	84.5879	259	312	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_905212365.1	s__Phascolarctobacterium_A sp905212365	79.3632	175	312	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	-
GCF_000188175.1	s__Phascolarctobacterium_A succinatutens	79.2492	150	312	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	-
GCA_000434895.1	s__Phascolarctobacterium_A succinatutens_A	79.2388	152	312	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	79.216	144	312	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_900552855.1	s__Phascolarctobacterium_A sp900552855	78.4704	82	312	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Phascolarctobacterium_A	95.0	99.31	98.81	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-04 18:00:48,724] [INFO] GTDB search result was written to GCA_004554325.1_ASM455432v1_genomic.fna/result_gtdb.tsv
[2023-06-04 18:00:48,725] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:00:48,728] [INFO] DFAST_QC result json was written to GCA_004554325.1_ASM455432v1_genomic.fna/dqc_result.json
[2023-06-04 18:00:48,728] [INFO] DFAST_QC completed!
[2023-06-04 18:00:48,729] [INFO] Total running time: 0h0m33s