[2024-01-24 11:19:48,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:48,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:48,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference
[2024-01-24 11:19:50,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,117] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg9aa94f57-380d-4918-8ad3-d63084b83af4/GCF_004340975.1_ASM434097v1_genomic.fna.gz | prodigal -d GCF_004340975.1_ASM434097v1_genomic.fna/cds.fna -a GCF_004340975.1_ASM434097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:19:56,773] [INFO] Task succeeded: Prodigal
[2024-01-24 11:19:56,773] [INFO] Task started: HMMsearch
[2024-01-24 11:19:56,774] [INFO] Running command: hmmsearch --tblout GCF_004340975.1_ASM434097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference/reference_markers.hmm GCF_004340975.1_ASM434097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:19:57,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:19:57,031] [INFO] Found 6/6 markers.
[2024-01-24 11:19:57,057] [INFO] Query marker FASTA was written to GCF_004340975.1_ASM434097v1_genomic.fna/markers.fasta
[2024-01-24 11:19:57,057] [INFO] Task started: Blastn
[2024-01-24 11:19:57,058] [INFO] Running command: blastn -query GCF_004340975.1_ASM434097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference/reference_markers.fasta -out GCF_004340975.1_ASM434097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:57,705] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:57,709] [INFO] Selected 24 target genomes.
[2024-01-24 11:19:57,710] [INFO] Target genome list was writen to GCF_004340975.1_ASM434097v1_genomic.fna/target_genomes.txt
[2024-01-24 11:19:57,738] [INFO] Task started: fastANI
[2024-01-24 11:19:57,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa94f57-380d-4918-8ad3-d63084b83af4/GCF_004340975.1_ASM434097v1_genomic.fna.gz --refList GCF_004340975.1_ASM434097v1_genomic.fna/target_genomes.txt --output GCF_004340975.1_ASM434097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:09,161] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:09,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:09,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:09,171] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:09,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:09,171] [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
Frisingicoccus caecimuris	strain=DSM 28559	GCA_004340975.1	1796636	1796636	type	True	100.0	884	886	95	conclusive
Frisingicoccus caecimuris	strain=DSM 28559	GCA_024622585.1	1796636	1796636	type	True	99.999	878	886	95	conclusive
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.2563	72	886	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.6124	59	886	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	77.2253	106	886	95	below_threshold
Coprococcus catus	strain=VPIC661	GCA_019734885.1	116085	116085	suspected-type	True	77.2185	106	886	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.1853	54	886	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.1219	53	886	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	76.8567	51	886	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.8068	52	886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:09,173] [INFO] DFAST Taxonomy check result was written to GCF_004340975.1_ASM434097v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:09,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:09,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:09,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference/checkm_data
[2024-01-24 11:20:09,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:09,209] [INFO] Task started: CheckM
[2024-01-24 11:20:09,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340975.1_ASM434097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340975.1_ASM434097v1_genomic.fna/checkm_input GCF_004340975.1_ASM434097v1_genomic.fna/checkm_result
[2024-01-24 11:20:35,196] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:35,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:35,218] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:35,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:35,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340975.1_ASM434097v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:35,219] [INFO] Task started: Blastn
[2024-01-24 11:20:35,220] [INFO] Running command: blastn -query GCF_004340975.1_ASM434097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ab8eb07-58d7-46e8-977e-65a203fa624c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340975.1_ASM434097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:36,277] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:36,281] [INFO] Selected 12 target genomes.
[2024-01-24 11:20:36,281] [INFO] Target genome list was writen to GCF_004340975.1_ASM434097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:36,289] [INFO] Task started: fastANI
[2024-01-24 11:20:36,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg9aa94f57-380d-4918-8ad3-d63084b83af4/GCF_004340975.1_ASM434097v1_genomic.fna.gz --refList GCF_004340975.1_ASM434097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340975.1_ASM434097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:42,233] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:42,246] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:42,247] [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_004340975.1	s__Frisingicoccus caecimuris	100.0	884	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	98.08	97.54	0.83	0.77	6	conclusive
GCA_900549105.1	s__Frisingicoccus sp900549105	82.3646	494	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.93	99.87	0.93	0.90	3	-
GCA_900753685.1	s__Frisingicoccus sp900753685	82.2483	372	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.11	98.62	0.83	0.76	3	-
GCA_002361775.1	s__Oliverpabstia sp002361775	81.481	63	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCA_016298055.1	s__Frisingicoccus sp016298055	79.644	265	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	95.75	95.75	0.73	0.73	2	-
GCA_900757195.1	s__Frisingicoccus sp900757195	79.3146	326	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.09	99.09	0.92	0.92	2	-
GCA_009929615.1	s__Frisingicoccus sp009929615	78.8663	318	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	99.91	99.91	0.88	0.88	2	-
GCA_017391465.1	s__Frisingicoccus sp017391465	78.3502	183	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Frisingicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902381825.1	s__Coprococcus_A catus	77.5203	104	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus_A	95.0	98.33	97.35	0.89	0.80	8	-
GCA_018711005.1	s__Catenibacillus faecigallinarum	77.2046	72	886	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Catenibacillus	95.0	99.82	99.82	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:42,249] [INFO] GTDB search result was written to GCF_004340975.1_ASM434097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:42,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:42,253] [INFO] DFAST_QC result json was written to GCF_004340975.1_ASM434097v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:42,254] [INFO] DFAST_QC completed!
[2024-01-24 11:20:42,254] [INFO] Total running time: 0h0m53s