[2024-01-24 12:53:49,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,419] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference
[2024-01-24 12:53:51,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,733] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg120e0756-b28c-4861-a227-ccb6b40c5ba7/GCF_000156175.1_ASM15617v1_genomic.fna.gz | prodigal -d GCF_000156175.1_ASM15617v1_genomic.fna/cds.fna -a GCF_000156175.1_ASM15617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:57,665] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:57,666] [INFO] Task started: HMMsearch
[2024-01-24 12:53:57,666] [INFO] Running command: hmmsearch --tblout GCF_000156175.1_ASM15617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference/reference_markers.hmm GCF_000156175.1_ASM15617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:57,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:57,896] [INFO] Found 6/6 markers.
[2024-01-24 12:53:57,915] [INFO] Query marker FASTA was written to GCF_000156175.1_ASM15617v1_genomic.fna/markers.fasta
[2024-01-24 12:53:57,915] [INFO] Task started: Blastn
[2024-01-24 12:53:57,916] [INFO] Running command: blastn -query GCF_000156175.1_ASM15617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference/reference_markers.fasta -out GCF_000156175.1_ASM15617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:58,642] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:58,646] [INFO] Selected 13 target genomes.
[2024-01-24 12:53:58,647] [INFO] Target genome list was writen to GCF_000156175.1_ASM15617v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:58,744] [INFO] Task started: fastANI
[2024-01-24 12:53:58,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg120e0756-b28c-4861-a227-ccb6b40c5ba7/GCF_000156175.1_ASM15617v1_genomic.fna.gz --refList GCF_000156175.1_ASM15617v1_genomic.fna/target_genomes.txt --output GCF_000156175.1_ASM15617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:05,075] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:05,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:05,076] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:05,089] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:05,090] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:05,090] [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
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	99.9999	601	601	95	conclusive
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	83.8107	417	601	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	83.7839	422	601	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	82.1563	312	601	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	81.306	243	601	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	80.7195	267	601	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.2234	256	601	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.7323	244	601	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	79.4754	236	601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:05,092] [INFO] DFAST Taxonomy check result was written to GCF_000156175.1_ASM15617v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:05,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:05,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:05,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference/checkm_data
[2024-01-24 12:54:05,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:05,114] [INFO] Task started: CheckM
[2024-01-24 12:54:05,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000156175.1_ASM15617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000156175.1_ASM15617v1_genomic.fna/checkm_input GCF_000156175.1_ASM15617v1_genomic.fna/checkm_result
[2024-01-24 12:54:28,064] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:28,067] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:28,084] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:28,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:28,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000156175.1_ASM15617v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:28,085] [INFO] Task started: Blastn
[2024-01-24 12:54:28,085] [INFO] Running command: blastn -query GCF_000156175.1_ASM15617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6fa62a4-2aea-4dff-8fa1-049488abe84e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000156175.1_ASM15617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:29,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:29,530] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:29,530] [INFO] Target genome list was writen to GCF_000156175.1_ASM15617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:29,557] [INFO] Task started: fastANI
[2024-01-24 12:54:29,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg120e0756-b28c-4861-a227-ccb6b40c5ba7/GCF_000156175.1_ASM15617v1_genomic.fna.gz --refList GCF_000156175.1_ASM15617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000156175.1_ASM15617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:33,888] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:33,898] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:33,899] [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_000156175.1	s__Collinsella intestinalis	99.9999	601	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.88	95.17	0.89	0.86	15	conclusive
GCA_900551665.1	s__Collinsella sp900551665	93.7416	430	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479805.1	s__Collinsella sp003479805	84.1131	400	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.77	98.33	0.94	0.90	6	-
GCF_000156215.1	s__Collinsella stercoris	83.8115	417	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.61	95.23	0.87	0.81	5	-
GCA_900540845.1	s__Collinsella sp900540845	83.6929	382	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900119895.1	s__Collinsella phocaeensis	82.1563	312	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCA_900764955.1	s__Collinsella sp900764955	81.855	110	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.99	96.94	0.60	0.58	3	-
GCF_008014645.1	s__Collinsella sp008014645	81.542	301	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.90	97.84	0.90	0.89	3	-
GCF_900199705.1	s__Collinsella provencensis	81.306	243	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.12	97.12	0.85	0.85	2	-
GCF_002232035.1	s__Collinsella sp002232035	79.9343	237	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0836	95.49	95.12	0.86	0.82	32	-
GCA_900554325.1	s__Collinsella sp900554325	79.5096	207	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:33,900] [INFO] GTDB search result was written to GCF_000156175.1_ASM15617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:33,901] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:33,905] [INFO] DFAST_QC result json was written to GCF_000156175.1_ASM15617v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:33,905] [INFO] DFAST_QC completed!
[2024-01-24 12:54:33,905] [INFO] Total running time: 0h0m44s