[2024-01-24 12:39:35,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference
[2024-01-24 12:39:36,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,681] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d0d4de1-d180-4a81-b557-0caa8142dcf6/GCF_004341945.1_ASM434194v1_genomic.fna.gz | prodigal -d GCF_004341945.1_ASM434194v1_genomic.fna/cds.fna -a GCF_004341945.1_ASM434194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:43,401] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:43,402] [INFO] Task started: HMMsearch
[2024-01-24 12:39:43,402] [INFO] Running command: hmmsearch --tblout GCF_004341945.1_ASM434194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference/reference_markers.hmm GCF_004341945.1_ASM434194v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:43,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:43,643] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3d0d4de1-d180-4a81-b557-0caa8142dcf6/GCF_004341945.1_ASM434194v1_genomic.fna.gz]
[2024-01-24 12:39:43,680] [INFO] Query marker FASTA was written to GCF_004341945.1_ASM434194v1_genomic.fna/markers.fasta
[2024-01-24 12:39:43,680] [INFO] Task started: Blastn
[2024-01-24 12:39:43,680] [INFO] Running command: blastn -query GCF_004341945.1_ASM434194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference/reference_markers.fasta -out GCF_004341945.1_ASM434194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:44,252] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:44,256] [INFO] Selected 16 target genomes.
[2024-01-24 12:39:44,257] [INFO] Target genome list was writen to GCF_004341945.1_ASM434194v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:44,263] [INFO] Task started: fastANI
[2024-01-24 12:39:44,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d0d4de1-d180-4a81-b557-0caa8142dcf6/GCF_004341945.1_ASM434194v1_genomic.fna.gz --refList GCF_004341945.1_ASM434194v1_genomic.fna/target_genomes.txt --output GCF_004341945.1_ASM434194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:51,619] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:51,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:51,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:51,630] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:39:51,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:51,631] [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
Longicatena caecimuris	strain=DSM 29481	GCA_004341945.1	1796635	1796635	type	True	100.0	956	956	95	conclusive
Longicatena caecimuris	strain=DSM 29481	GCA_024622185.1	1796635	1796635	type	True	99.9944	951	956	95	conclusive
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	78.5679	168	956	95	below_threshold
[Clostridium] innocuum	strain=ATCC 14501	GCA_012317185.1	1522	1522	type	True	78.1321	158	956	95	below_threshold
[Clostridium] innocuum	strain=ATCC 14501	GCA_018458805.1	1522	1522	type	True	78.0875	157	956	95	below_threshold
Copranaerobaculum intestinale	strain=DONG20-135	GCA_009831105.1	2692629	2692629	type	True	77.9086	57	956	95	below_threshold
Amedibacillus dolichus	strain=DSM 3991	GCA_000154285.1	31971	31971	type	True	77.7231	115	956	95	below_threshold
Merdibacter massiliensis	strain=Marseille-P3254	GCA_900155395.1	1871030	1871030	type	True	77.3961	78	956	95	below_threshold
Traorella massiliensis	strain=Marseille-P3110	GCA_900104665.1	1903263	1903263	type	True	76.7536	51	956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:51,632] [INFO] DFAST Taxonomy check result was written to GCF_004341945.1_ASM434194v1_genomic.fna/tc_result.tsv
[2024-01-24 12:39:51,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:51,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:51,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference/checkm_data
[2024-01-24 12:39:51,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:51,669] [INFO] Task started: CheckM
[2024-01-24 12:39:51,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341945.1_ASM434194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341945.1_ASM434194v1_genomic.fna/checkm_input GCF_004341945.1_ASM434194v1_genomic.fna/checkm_result
[2024-01-24 12:40:18,344] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:18,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:18,371] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:18,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:18,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341945.1_ASM434194v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:18,372] [INFO] Task started: Blastn
[2024-01-24 12:40:18,372] [INFO] Running command: blastn -query GCF_004341945.1_ASM434194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84257d86-f6dd-4085-a556-f35b9f14903f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341945.1_ASM434194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:19,232] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:19,235] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:19,236] [INFO] Target genome list was writen to GCF_004341945.1_ASM434194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:19,249] [INFO] Task started: fastANI
[2024-01-24 12:40:19,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d0d4de1-d180-4a81-b557-0caa8142dcf6/GCF_004341945.1_ASM434194v1_genomic.fna.gz --refList GCF_004341945.1_ASM434194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341945.1_ASM434194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:27,487] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:27,498] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:27,498] [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_004341945.1	s__Longicatena caecimuris	100.0	956	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longicatena	95.0	98.56	98.14	0.91	0.88	21	conclusive
GCA_003481775.1	s__Clostridium_AQ sp003481775	78.9335	178	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.27	97.98	0.91	0.82	5	-
GCA_910576855.1	s__C-19 sp910576855	78.7654	69	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__C-19	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014337235.1	s__NSJ-61 sp003433845	78.6274	194	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	-
GCF_010537335.1	s__Amedibacterium intestinale	78.5529	165	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	98.96	98.46	0.86	0.72	14	-
GCA_900552125.1	s__Clostridium_AQ sp900552125	78.482	141	956	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_017161075.1	s__Clostridium_AQ sp000165065	78.14	154	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.84	97.80	0.84	0.80	7	-
GCF_012317185.1	s__Clostridium_AQ innocuum	78.1246	159	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	97.93	97.20	0.87	0.81	50	-
GCA_904395785.1	s__Amedibacterium sp904395785	78.0264	83	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154285.1	s__Amedibacillus dolichus	77.7377	115	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacillus	95.0	99.06	98.73	0.91	0.85	7	-
GCF_900155395.1	s__Merdibacter massiliensis	77.3961	78	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Merdibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902399855.1	s__Faecalicoccus sp900546545	77.2598	51	956	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	99.03	98.24	0.89	0.80	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:27,500] [INFO] GTDB search result was written to GCF_004341945.1_ASM434194v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:27,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:27,505] [INFO] DFAST_QC result json was written to GCF_004341945.1_ASM434194v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:27,505] [INFO] DFAST_QC completed!
[2024-01-24 12:40:27,505] [INFO] Total running time: 0h0m52s