[2024-01-24 13:58:10,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference
[2024-01-24 13:58:12,147] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,148] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,148] [INFO] Running command: gunzip -c /var/lib/cwl/stga6fb1eb9-96f1-4ac5-bf6e-847bf54f71be/GCF_014337235.1_ASM1433723v1_genomic.fna.gz | prodigal -d GCF_014337235.1_ASM1433723v1_genomic.fna/cds.fna -a GCF_014337235.1_ASM1433723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:21,613] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:21,614] [INFO] Task started: HMMsearch
[2024-01-24 13:58:21,614] [INFO] Running command: hmmsearch --tblout GCF_014337235.1_ASM1433723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference/reference_markers.hmm GCF_014337235.1_ASM1433723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:21,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:21,911] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga6fb1eb9-96f1-4ac5-bf6e-847bf54f71be/GCF_014337235.1_ASM1433723v1_genomic.fna.gz]
[2024-01-24 13:58:21,947] [INFO] Query marker FASTA was written to GCF_014337235.1_ASM1433723v1_genomic.fna/markers.fasta
[2024-01-24 13:58:21,947] [INFO] Task started: Blastn
[2024-01-24 13:58:21,947] [INFO] Running command: blastn -query GCF_014337235.1_ASM1433723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference/reference_markers.fasta -out GCF_014337235.1_ASM1433723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:22,612] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,615] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:22,616] [INFO] Target genome list was writen to GCF_014337235.1_ASM1433723v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:22,624] [INFO] Task started: fastANI
[2024-01-24 13:58:22,625] [INFO] Running command: fastANI --query /var/lib/cwl/stga6fb1eb9-96f1-4ac5-bf6e-847bf54f71be/GCF_014337235.1_ASM1433723v1_genomic.fna.gz --refList GCF_014337235.1_ASM1433723v1_genomic.fna/target_genomes.txt --output GCF_014337235.1_ASM1433723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:33,716] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:33,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:33,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:33,730] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:33,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:33,730] [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
Copranaerobaculum intestinale	strain=DONG20-135	GCA_009831105.1	2692629	2692629	type	True	81.9245	66	1293	95	below_threshold
Dielma fastidiosa	strain=JC13	GCA_000313565.2	1034346	1034346	type	True	80.463	87	1293	95	below_threshold
[Clostridium] innocuum	strain=ATCC 14501	GCA_012317185.1	1522	1522	type	True	80.4409	153	1293	95	below_threshold
[Clostridium] innocuum	strain=ATCC 14501	GCA_018458805.1	1522	1522	type	True	80.2885	152	1293	95	below_threshold
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	79.8754	169	1293	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_024622185.1	1796635	1796635	type	True	79.1778	176	1293	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_004341945.1	1796635	1796635	type	True	79.0428	185	1293	95	below_threshold
Amedibacillus dolichus	strain=DSM 3991	GCA_000154285.1	31971	31971	type	True	78.9515	117	1293	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	76.8297	56	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:33,732] [INFO] DFAST Taxonomy check result was written to GCF_014337235.1_ASM1433723v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:33,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:33,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:33,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference/checkm_data
[2024-01-24 13:58:33,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:33,772] [INFO] Task started: CheckM
[2024-01-24 13:58:33,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014337235.1_ASM1433723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014337235.1_ASM1433723v1_genomic.fna/checkm_input GCF_014337235.1_ASM1433723v1_genomic.fna/checkm_result
[2024-01-24 13:59:06,357] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:06,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 9.90%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,378] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:06,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:06,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014337235.1_ASM1433723v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:06,379] [INFO] Task started: Blastn
[2024-01-24 13:59:06,380] [INFO] Running command: blastn -query GCF_014337235.1_ASM1433723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c5eaf44-f959-4d2b-9da4-dc2e06364f2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014337235.1_ASM1433723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,210] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:07,211] [INFO] Target genome list was writen to GCF_014337235.1_ASM1433723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:07,241] [INFO] Task started: fastANI
[2024-01-24 13:59:07,241] [INFO] Running command: fastANI --query /var/lib/cwl/stga6fb1eb9-96f1-4ac5-bf6e-847bf54f71be/GCF_014337235.1_ASM1433723v1_genomic.fna.gz --refList GCF_014337235.1_ASM1433723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014337235.1_ASM1433723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:17,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:17,214] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:17,214] [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_014337235.1	s__NSJ-61 sp003433845	100.0	1291	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	conclusive
GCA_003481775.1	s__Clostridium_AQ sp003481775	82.8925	166	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.27	97.98	0.91	0.82	5	-
GCF_012317185.1	s__Clostridium_AQ innocuum	80.4275	155	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.93	97.20	0.87	0.81	50	-
GCF_010537335.1	s__Amedibacterium intestinale	80.0191	168	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	-
GCF_004341945.1	s__Longicatena caecimuris	79.092	182	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longicatena	95.0	98.56	98.14	0.91	0.88	21	-
GCF_000154285.1	s__Amedibacillus dolichus	79.0568	119	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacillus	95.0	99.06	98.73	0.91	0.85	7	-
GCF_000156655.1	s__Holdemanella biformis	78.9275	64	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
GCA_017161075.1	s__Clostridium_AQ sp000165065	78.6428	152	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.84	97.80	0.84	0.80	7	-
GCA_910575705.1	s__CAJTFG01 sp910575705	78.3626	54	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__CAJTFG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552125.1	s__Clostridium_AQ sp900552125	78.1748	180	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.93	99.93	0.86	0.86	2	-
GCA_904395785.1	s__Amedibacterium sp904395785	77.7338	98	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003458715.1	s__Holdemanella sp003458715	77.345	54	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
GCF_009696175.1	s__Floccifex porci	76.8297	56	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex	95.0	99.09	99.09	0.94	0.94	2	-
GCA_900547815.1	s__Holdemanella sp900547815	76.4695	52	1293	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,216] [INFO] GTDB search result was written to GCF_014337235.1_ASM1433723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:17,217] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:17,221] [INFO] DFAST_QC result json was written to GCF_014337235.1_ASM1433723v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:17,221] [INFO] DFAST_QC completed!
[2024-01-24 13:59:17,221] [INFO] Total running time: 0h1m6s