[2024-01-25 17:47:50,463] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:50,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:50,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference
[2024-01-25 17:47:51,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:51,611] [INFO] Task started: Prodigal
[2024-01-25 17:47:51,611] [INFO] Running command: gunzip -c /var/lib/cwl/stg79be156c-9cef-43c3-be0f-d1c56b23d359/GCF_025149625.1_ASM2514962v1_genomic.fna.gz | prodigal -d GCF_025149625.1_ASM2514962v1_genomic.fna/cds.fna -a GCF_025149625.1_ASM2514962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:58,766] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:58,766] [INFO] Task started: HMMsearch
[2024-01-25 17:47:58,766] [INFO] Running command: hmmsearch --tblout GCF_025149625.1_ASM2514962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference/reference_markers.hmm GCF_025149625.1_ASM2514962v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:58,947] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:58,948] [INFO] Found 6/6 markers.
[2024-01-25 17:47:58,968] [INFO] Query marker FASTA was written to GCF_025149625.1_ASM2514962v1_genomic.fna/markers.fasta
[2024-01-25 17:47:58,969] [INFO] Task started: Blastn
[2024-01-25 17:47:58,969] [INFO] Running command: blastn -query GCF_025149625.1_ASM2514962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference/reference_markers.fasta -out GCF_025149625.1_ASM2514962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:59,589] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:59,593] [INFO] Selected 14 target genomes.
[2024-01-25 17:47:59,593] [INFO] Target genome list was writen to GCF_025149625.1_ASM2514962v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:59,600] [INFO] Task started: fastANI
[2024-01-25 17:47:59,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg79be156c-9cef-43c3-be0f-d1c56b23d359/GCF_025149625.1_ASM2514962v1_genomic.fna.gz --refList GCF_025149625.1_ASM2514962v1_genomic.fna/target_genomes.txt --output GCF_025149625.1_ASM2514962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:06,872] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:06,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:06,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:06,880] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:48:06,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:06,881] [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 stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	100.0	819	820	95	conclusive
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	99.8427	799	820	95	conclusive
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	83.7822	418	820	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	82.5199	361	820	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	80.9187	284	820	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	80.659	290	820	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	80.5152	290	820	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	80.4935	317	820	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	80.3799	284	820	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	80.3208	293	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:06,882] [INFO] DFAST Taxonomy check result was written to GCF_025149625.1_ASM2514962v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:06,883] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:06,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:06,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference/checkm_data
[2024-01-25 17:48:06,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:06,911] [INFO] Task started: CheckM
[2024-01-25 17:48:06,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025149625.1_ASM2514962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025149625.1_ASM2514962v1_genomic.fna/checkm_input GCF_025149625.1_ASM2514962v1_genomic.fna/checkm_result
[2024-01-25 17:48:31,097] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:31,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:31,127] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:31,128] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:31,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025149625.1_ASM2514962v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:31,128] [INFO] Task started: Blastn
[2024-01-25 17:48:31,129] [INFO] Running command: blastn -query GCF_025149625.1_ASM2514962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9aea8e6c-a700-46b5-a05e-f0d7b3a1ab5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025149625.1_ASM2514962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:32,236] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:32,239] [INFO] Selected 10 target genomes.
[2024-01-25 17:48:32,239] [INFO] Target genome list was writen to GCF_025149625.1_ASM2514962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:32,248] [INFO] Task started: fastANI
[2024-01-25 17:48:32,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg79be156c-9cef-43c3-be0f-d1c56b23d359/GCF_025149625.1_ASM2514962v1_genomic.fna.gz --refList GCF_025149625.1_ASM2514962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025149625.1_ASM2514962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:37,066] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:37,073] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:37,073] [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_000156215.1	s__Collinsella stercoris	99.8427	799	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.61	95.23	0.87	0.81	5	conclusive
GCF_003479805.1	s__Collinsella sp003479805	84.8917	476	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.77	98.33	0.94	0.90	6	-
GCA_900540845.1	s__Collinsella sp900540845	84.0798	418	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000156175.1	s__Collinsella intestinalis	83.8236	419	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.88	95.17	0.89	0.86	15	-
GCA_900551665.1	s__Collinsella sp900551665	83.7151	355	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764955.1	s__Collinsella sp900764955	82.6748	114	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.99	96.94	0.60	0.58	3	-
GCF_900119895.1	s__Collinsella phocaeensis	82.4986	362	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.56	95.56	0.87	0.87	2	-
GCF_008014645.1	s__Collinsella sp008014645	81.4118	319	820	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	80.9187	284	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.12	97.12	0.85	0.85	2	-
GCA_902362275.1	s__Collinsella sp902362275	80.3077	287	820	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.48	97.28	0.91	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:37,075] [INFO] GTDB search result was written to GCF_025149625.1_ASM2514962v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:37,075] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:37,078] [INFO] DFAST_QC result json was written to GCF_025149625.1_ASM2514962v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:37,078] [INFO] DFAST_QC completed!
[2024-01-25 17:48:37,078] [INFO] Total running time: 0h0m47s