[2024-01-25 18:50:20,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:20,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:20,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference
[2024-01-25 18:50:21,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:21,710] [INFO] Task started: Prodigal
[2024-01-25 18:50:21,710] [INFO] Running command: gunzip -c /var/lib/cwl/stge586222d-e701-4215-a5d8-d4b6b400eca6/GCF_001494635.1_ASM149463v1_genomic.fna.gz | prodigal -d GCF_001494635.1_ASM149463v1_genomic.fna/cds.fna -a GCF_001494635.1_ASM149463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:28,933] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:28,933] [INFO] Task started: HMMsearch
[2024-01-25 18:50:28,934] [INFO] Running command: hmmsearch --tblout GCF_001494635.1_ASM149463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference/reference_markers.hmm GCF_001494635.1_ASM149463v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:29,094] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:29,095] [INFO] Found 6/6 markers.
[2024-01-25 18:50:29,115] [INFO] Query marker FASTA was written to GCF_001494635.1_ASM149463v1_genomic.fna/markers.fasta
[2024-01-25 18:50:29,115] [INFO] Task started: Blastn
[2024-01-25 18:50:29,115] [INFO] Running command: blastn -query GCF_001494635.1_ASM149463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference/reference_markers.fasta -out GCF_001494635.1_ASM149463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:29,715] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:29,718] [INFO] Selected 15 target genomes.
[2024-01-25 18:50:29,719] [INFO] Target genome list was writen to GCF_001494635.1_ASM149463v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:29,724] [INFO] Task started: fastANI
[2024-01-25 18:50:29,724] [INFO] Running command: fastANI --query /var/lib/cwl/stge586222d-e701-4215-a5d8-d4b6b400eca6/GCF_001494635.1_ASM149463v1_genomic.fna.gz --refList GCF_001494635.1_ASM149463v1_genomic.fna/target_genomes.txt --output GCF_001494635.1_ASM149463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:37,296] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:37,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:37,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:37,306] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:50:37,306] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:50:37,306] [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
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.8847	298	816	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.8736	265	816	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.6966	297	816	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.5455	254	816	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.4358	260	816	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.2644	214	816	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	79.0938	227	816	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	79.0711	221	816	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	79.006	221	816	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	78.8286	246	816	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.824	245	816	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	77.7378	152	816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:37,308] [INFO] DFAST Taxonomy check result was written to GCF_001494635.1_ASM149463v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:37,309] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:37,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:37,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference/checkm_data
[2024-01-25 18:50:37,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:37,339] [INFO] Task started: CheckM
[2024-01-25 18:50:37,339] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001494635.1_ASM149463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001494635.1_ASM149463v1_genomic.fna/checkm_input GCF_001494635.1_ASM149463v1_genomic.fna/checkm_result
[2024-01-25 18:51:01,408] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:01,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:01,434] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:01,435] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:01,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001494635.1_ASM149463v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:01,435] [INFO] Task started: Blastn
[2024-01-25 18:51:01,435] [INFO] Running command: blastn -query GCF_001494635.1_ASM149463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a6c5382-a63a-4692-ae21-1c4bff182d5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001494635.1_ASM149463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:02,382] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:02,387] [INFO] Selected 9 target genomes.
[2024-01-25 18:51:02,387] [INFO] Target genome list was writen to GCF_001494635.1_ASM149463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:02,422] [INFO] Task started: fastANI
[2024-01-25 18:51:02,423] [INFO] Running command: fastANI --query /var/lib/cwl/stge586222d-e701-4215-a5d8-d4b6b400eca6/GCF_001494635.1_ASM149463v1_genomic.fna.gz --refList GCF_001494635.1_ASM149463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001494635.1_ASM149463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:07,860] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:07,867] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:07,868] [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_001494635.1	s__Tractidigestivibacter scatoligenes	100.0	814	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900119625.1	s__Tractidigestivibacter sp900119625	94.7948	660	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	96.91	96.91	0.78	0.78	2	-
GCA_902834555.1	s__Tractidigestivibacter sp902834555	92.0053	653	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	91.5213	635	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_902773995.1	s__Tractidigestivibacter sp902773995	90.8768	566	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.13	97.55	0.87	0.83	4	-
GCA_900768455.1	s__Tractidigestivibacter sp900768455	90.6848	523	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	97.35	97.35	0.93	0.93	2	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	90.4944	412	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111695.1	s__Tractidigestivibacter sp900111695	89.2083	641	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	86.4611	534	816	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:07,870] [INFO] GTDB search result was written to GCF_001494635.1_ASM149463v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:07,870] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:07,873] [INFO] DFAST_QC result json was written to GCF_001494635.1_ASM149463v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:07,873] [INFO] DFAST_QC completed!
[2024-01-25 18:51:07,873] [INFO] Total running time: 0h0m47s