[2024-01-24 14:30:31,210] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,212] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference
[2024-01-24 14:30:33,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,805] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgd962dcb2-1f4b-4f98-af51-0f7e41add226/GCF_004216775.1_ASM421677v1_genomic.fna.gz | prodigal -d GCF_004216775.1_ASM421677v1_genomic.fna/cds.fna -a GCF_004216775.1_ASM421677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:43,307] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:43,308] [INFO] Task started: HMMsearch
[2024-01-24 14:30:43,308] [INFO] Running command: hmmsearch --tblout GCF_004216775.1_ASM421677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference/reference_markers.hmm GCF_004216775.1_ASM421677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:43,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:43,668] [INFO] Found 6/6 markers.
[2024-01-24 14:30:43,704] [INFO] Query marker FASTA was written to GCF_004216775.1_ASM421677v1_genomic.fna/markers.fasta
[2024-01-24 14:30:43,705] [INFO] Task started: Blastn
[2024-01-24 14:30:43,705] [INFO] Running command: blastn -query GCF_004216775.1_ASM421677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference/reference_markers.fasta -out GCF_004216775.1_ASM421677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:44,397] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:44,401] [INFO] Selected 25 target genomes.
[2024-01-24 14:30:44,401] [INFO] Target genome list was writen to GCF_004216775.1_ASM421677v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:44,448] [INFO] Task started: fastANI
[2024-01-24 14:30:44,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgd962dcb2-1f4b-4f98-af51-0f7e41add226/GCF_004216775.1_ASM421677v1_genomic.fna.gz --refList GCF_004216775.1_ASM421677v1_genomic.fna/target_genomes.txt --output GCF_004216775.1_ASM421677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:03,523] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:03,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:03,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:03,533] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:03,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:03,534] [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
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	100.0	1145	1145	95	conclusive
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.03	53	1145	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.6465	79	1145	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.6459	57	1145	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.4934	79	1145	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.4452	87	1145	95	below_threshold
Qiania dongpingensis	strain=NSJ-38	GCA_014337195.1	2763669	2763669	type	True	76.3453	71	1145	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.1825	59	1145	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.0628	66	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,535] [INFO] DFAST Taxonomy check result was written to GCF_004216775.1_ASM421677v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:03,536] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:03,536] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:03,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference/checkm_data
[2024-01-24 14:31:03,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:03,575] [INFO] Task started: CheckM
[2024-01-24 14:31:03,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216775.1_ASM421677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216775.1_ASM421677v1_genomic.fna/checkm_input GCF_004216775.1_ASM421677v1_genomic.fna/checkm_result
[2024-01-24 14:31:36,311] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:36,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:36,333] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:36,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:36,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216775.1_ASM421677v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:36,334] [INFO] Task started: Blastn
[2024-01-24 14:31:36,334] [INFO] Running command: blastn -query GCF_004216775.1_ASM421677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25882535-0787-48d7-8739-98c659c46039/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216775.1_ASM421677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:37,448] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:37,451] [INFO] Selected 29 target genomes.
[2024-01-24 14:31:37,452] [INFO] Target genome list was writen to GCF_004216775.1_ASM421677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:37,521] [INFO] Task started: fastANI
[2024-01-24 14:31:37,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgd962dcb2-1f4b-4f98-af51-0f7e41add226/GCF_004216775.1_ASM421677v1_genomic.fna.gz --refList GCF_004216775.1_ASM421677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216775.1_ASM421677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:53,186] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:53,199] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:53,199] [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_004216775.1	s__Cuneatibacter caecimuris	100.0	1145	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Cuneatibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900538475.1	s__Ventrimonas sp900538475	76.759	59	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCA_910584375.1	s__Acetatifactor sp910584375	76.6365	62	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540335.1	s__Ventrimonas sp900540335	76.5101	50	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_019119775.1	s__Lachnoclostridium_A pullistercoris	76.4109	54	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.96	99.96	0.95	0.95	2	-
GCA_014337195.1	s__Paralachnospira sp014337195	76.3453	71	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363445.1	s__Paralachnospira sp902363445	76.2735	63	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716305.1	s__Scatomonas merdigallinarum	76.2465	60	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.11	99.10	0.93	0.92	3	-
GCA_910584585.1	s__14-2 sp910584585	76.2409	54	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018380885.1	s__Enterocloster sp900555905	76.2112	83	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_018711275.1	s__Pullilachnospira intestinigallinarum	76.2075	65	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	99.92	99.92	0.90	0.90	2	-
GCA_019119815.1	s__Eisenbergiella intestinipullorum	75.8563	61	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.95	99.95	0.93	0.93	2	-
GCA_018378255.1	s__CHH4-2 sp018378255	75.8478	65	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713515.1	s__Scatomonas pullistercoris	75.8363	66	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Scatomonas	95.0	99.97	99.97	0.94	0.94	2	-
GCA_904420225.1	s__Fimimorpha sp904420225	75.7813	50	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Fimimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403845.2	s__14-2 sp000403845	75.6938	67	1145	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:53,201] [INFO] GTDB search result was written to GCF_004216775.1_ASM421677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:53,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:53,207] [INFO] DFAST_QC result json was written to GCF_004216775.1_ASM421677v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:53,208] [INFO] DFAST_QC completed!
[2024-01-24 14:31:53,208] [INFO] Total running time: 0h1m22s