[2024-01-24 13:09:51,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference
[2024-01-24 13:09:53,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,196] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,196] [INFO] Running command: gunzip -c /var/lib/cwl/stg0830f645-0361-4f23-9e2e-11c6f8ce5c9d/GCF_004801635.1_ASM480163v1_genomic.fna.gz | prodigal -d GCF_004801635.1_ASM480163v1_genomic.fna/cds.fna -a GCF_004801635.1_ASM480163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:05,776] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:05,776] [INFO] Task started: HMMsearch
[2024-01-24 13:10:05,776] [INFO] Running command: hmmsearch --tblout GCF_004801635.1_ASM480163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference/reference_markers.hmm GCF_004801635.1_ASM480163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:06,082] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:06,083] [INFO] Found 6/6 markers.
[2024-01-24 13:10:06,106] [INFO] Query marker FASTA was written to GCF_004801635.1_ASM480163v1_genomic.fna/markers.fasta
[2024-01-24 13:10:06,106] [INFO] Task started: Blastn
[2024-01-24 13:10:06,106] [INFO] Running command: blastn -query GCF_004801635.1_ASM480163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference/reference_markers.fasta -out GCF_004801635.1_ASM480163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:06,737] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:06,740] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:06,741] [INFO] Target genome list was writen to GCF_004801635.1_ASM480163v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:06,747] [INFO] Task started: fastANI
[2024-01-24 13:10:06,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg0830f645-0361-4f23-9e2e-11c6f8ce5c9d/GCF_004801635.1_ASM480163v1_genomic.fna.gz --refList GCF_004801635.1_ASM480163v1_genomic.fna/target_genomes.txt --output GCF_004801635.1_ASM480163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:20,585] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:20,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:20,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:20,594] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:20,594] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:20,594] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	80.2892	61	692	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	79.5241	63	692	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	79.4922	102	692	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	78.6671	68	692	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	78.2652	78	692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:20,596] [INFO] DFAST Taxonomy check result was written to GCF_004801635.1_ASM480163v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:20,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:20,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:20,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference/checkm_data
[2024-01-24 13:10:20,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:20,628] [INFO] Task started: CheckM
[2024-01-24 13:10:20,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801635.1_ASM480163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801635.1_ASM480163v1_genomic.fna/checkm_input GCF_004801635.1_ASM480163v1_genomic.fna/checkm_result
[2024-01-24 13:10:59,436] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:59,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:59,458] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:59,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:59,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801635.1_ASM480163v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:59,459] [INFO] Task started: Blastn
[2024-01-24 13:10:59,459] [INFO] Running command: blastn -query GCF_004801635.1_ASM480163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bfaab1b-0416-48f1-b96b-85ec56730701/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801635.1_ASM480163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:00,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:00,274] [INFO] Selected 26 target genomes.
[2024-01-24 13:11:00,274] [INFO] Target genome list was writen to GCF_004801635.1_ASM480163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:00,293] [INFO] Task started: fastANI
[2024-01-24 13:11:00,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg0830f645-0361-4f23-9e2e-11c6f8ce5c9d/GCF_004801635.1_ASM480163v1_genomic.fna.gz --refList GCF_004801635.1_ASM480163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801635.1_ASM480163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:10,826] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:10,836] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:10,836] [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_004801635.1	s__Muribaculum sp002473395	100.0	688	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.14	99.05	0.85	0.79	8	conclusive
GCA_003762715.1	s__Paramuribaculum sp001689565	79.2402	74	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.89	98.71	0.85	0.83	3	-
GCF_004803695.1	s__Muribaculum gordoncarteri	78.2652	78	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	96.82	95.63	0.92	0.83	15	-
GCF_004570975.1	s__Muribaculum sp001701195	77.944	77	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.86	97.86	0.92	0.92	2	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	77.1294	67	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCA_003150235.1	s__Muribaculum sp003150235	76.8456	59	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	-
GCA_910578785.1	s__Muribaculum sp910578785	76.8068	57	692	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:10,838] [INFO] GTDB search result was written to GCF_004801635.1_ASM480163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:10,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:10,841] [INFO] DFAST_QC result json was written to GCF_004801635.1_ASM480163v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:10,841] [INFO] DFAST_QC completed!
[2024-01-24 13:11:10,841] [INFO] Total running time: 0h1m19s