[2024-01-24 13:58:55,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,590] [INFO] DQC Reference Directory: /var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference
[2024-01-24 13:58:56,952] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:56,953] [INFO] Task started: Prodigal
[2024-01-24 13:58:56,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg405ae99a-98bb-4031-a1ff-939e1576868c/GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/cds.fna -a GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:06,518] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:06,519] [INFO] Task started: HMMsearch
[2024-01-24 13:59:06,519] [INFO] Running command: hmmsearch --tblout GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference/reference_markers.hmm GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:06,783] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:06,785] [INFO] Found 6/6 markers.
[2024-01-24 13:59:06,811] [INFO] Query marker FASTA was written to GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:59:06,811] [INFO] Task started: Blastn
[2024-01-24 13:59:06,811] [INFO] Running command: blastn -query GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference/reference_markers.fasta -out GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,529] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:07,529] [INFO] Target genome list was writen to GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:59:07,549] [INFO] Task started: fastANI
[2024-01-24 13:59:07,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg405ae99a-98bb-4031-a1ff-939e1576868c/GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna.gz --refList GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:12,726] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:12,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:12,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:12,742] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:12,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:12,742] [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
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	81.1943	398	1033	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	81.1373	415	1033	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	80.3531	283	1033	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	80.1755	282	1033	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	80.0003	290	1033	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	79.1583	197	1033	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.8899	198	1033	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:12,744] [INFO] DFAST Taxonomy check result was written to GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:59:12,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:12,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:12,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference/checkm_data
[2024-01-24 13:59:12,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:12,785] [INFO] Task started: CheckM
[2024-01-24 13:59:12,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/checkm_input GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:44,346] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:44,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:44,368] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:44,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:44,369] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:44,370] [INFO] Task started: Blastn
[2024-01-24 13:59:44,370] [INFO] Running command: blastn -query GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge4440a59-754b-45d1-b97b-6bbf253df5b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:45,649] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:45,652] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:45,653] [INFO] Target genome list was writen to GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:45,672] [INFO] Task started: fastANI
[2024-01-24 13:59:45,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg405ae99a-98bb-4031-a1ff-939e1576868c/GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna.gz --refList GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:52,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:52,638] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:52,638] [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_900167555.1	s__Gemmiger formicilis	100.0	1023	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.67	96.73	0.89	0.78	43	conclusive
GCF_018784445.1	s__Gemmiger sp900540775	88.0061	778	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.04	97.97	0.87	0.81	8	-
GCA_900540595.1	s__Gemmiger sp900540595	87.6373	661	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.09	95.97	0.86	0.82	4	-
GCA_900554145.1	s__Gemmiger sp900554145	85.7421	497	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.15	98.15	0.80	0.80	2	-
GCA_004554775.1	s__Gemmiger variabilis_B	83.9324	598	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.40	97.89	0.89	0.88	3	-
GCA_900539695.1	s__Gemmiger sp900539695	83.6765	540	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.42	97.91	0.86	0.79	8	-
GCA_004552305.1	s__Gemmiger variabilis_A	82.0334	421	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.82	96.59	0.82	0.70	4	-
GCA_003343905.1	s__Gemmiger variabilis_C	80.8682	419	1033	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:52,640] [INFO] GTDB search result was written to GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:52,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:52,644] [INFO] DFAST_QC result json was written to GCF_900167555.1_IMG-taxon_2590828806_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:52,644] [INFO] DFAST_QC completed!
[2024-01-24 13:59:52,645] [INFO] Total running time: 0h0m57s