[2024-01-24 13:49:54,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:54,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:54,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference
[2024-01-24 13:49:56,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,042] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e3553f4-59ab-4642-b304-68404e49451b/GCF_014334055.1_ASM1433405v1_genomic.fna.gz | prodigal -d GCF_014334055.1_ASM1433405v1_genomic.fna/cds.fna -a GCF_014334055.1_ASM1433405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:03,676] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:03,677] [INFO] Task started: HMMsearch
[2024-01-24 13:50:03,677] [INFO] Running command: hmmsearch --tblout GCF_014334055.1_ASM1433405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference/reference_markers.hmm GCF_014334055.1_ASM1433405v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:03,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:03,881] [INFO] Found 6/6 markers.
[2024-01-24 13:50:03,903] [INFO] Query marker FASTA was written to GCF_014334055.1_ASM1433405v1_genomic.fna/markers.fasta
[2024-01-24 13:50:03,904] [INFO] Task started: Blastn
[2024-01-24 13:50:03,904] [INFO] Running command: blastn -query GCF_014334055.1_ASM1433405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference/reference_markers.fasta -out GCF_014334055.1_ASM1433405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:04,535] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:04,537] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:04,537] [INFO] Target genome list was writen to GCF_014334055.1_ASM1433405v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:04,543] [INFO] Task started: fastANI
[2024-01-24 13:50:04,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e3553f4-59ab-4642-b304-68404e49451b/GCF_014334055.1_ASM1433405v1_genomic.fna.gz --refList GCF_014334055.1_ASM1433405v1_genomic.fna/target_genomes.txt --output GCF_014334055.1_ASM1433405v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:11,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:11,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:11,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:11,980] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:11,980] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:11,981] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	91.2371	736	941	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	80.5098	145	941	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	80.1515	133	941	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	80.0888	141	941	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	79.9479	175	941	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.601	233	941	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.5872	359	941	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	79.0605	186	941	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.7218	176	941	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.69	178	941	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.6248	214	941	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.431	209	941	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.4106	196	941	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.3382	93	941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:11,982] [INFO] DFAST Taxonomy check result was written to GCF_014334055.1_ASM1433405v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:11,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:11,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:11,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference/checkm_data
[2024-01-24 13:50:11,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:12,011] [INFO] Task started: CheckM
[2024-01-24 13:50:12,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014334055.1_ASM1433405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014334055.1_ASM1433405v1_genomic.fna/checkm_input GCF_014334055.1_ASM1433405v1_genomic.fna/checkm_result
[2024-01-24 13:50:37,269] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:37,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,285] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:37,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:37,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014334055.1_ASM1433405v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:37,285] [INFO] Task started: Blastn
[2024-01-24 13:50:37,285] [INFO] Running command: blastn -query GCF_014334055.1_ASM1433405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d940ea1-c73c-4fe5-9db0-75da9ac76331/dqc_reference/reference_markers_gtdb.fasta -out GCF_014334055.1_ASM1433405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,488] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:38,488] [INFO] Target genome list was writen to GCF_014334055.1_ASM1433405v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:38,508] [INFO] Task started: fastANI
[2024-01-24 13:50:38,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e3553f4-59ab-4642-b304-68404e49451b/GCF_014334055.1_ASM1433405v1_genomic.fna.gz --refList GCF_014334055.1_ASM1433405v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014334055.1_ASM1433405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:48,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:48,165] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:48,165] [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_014334055.1	s__NSJ-62 sp014334055	100.0	941	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-62	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018919205.1	s__NSJ-62 sp018919205	91.2371	736	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-62	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	80.1592	333	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCF_018228705.1	s__Dysosmobacter sp018228705	80.0892	368	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118505.1	s__Dysosmobacter excrementavium	79.6773	306	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018408705.1	s__Dysosmobacter sp014297375	79.6556	234	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.15	98.99	0.84	0.71	5	-
GCA_900770295.1	s__Dysosmobacter sp900770295	79.5186	298	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548505.1	s__Dysosmobacter sp900548505	79.5041	243	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546705.1	s__Dysosmobacter sp900546705	79.4328	250	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469475.1	s__Dysosmobacter sp017469475	79.3875	252	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.68	97.62	0.84	0.82	4	-
GCF_002161215.1	s__Flavonifractor avistercoris	79.2675	210	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_900199495.1	s__An92 sp900199495	78.9368	187	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCA_900545495.1	s__CAG-83 sp900545495	78.8681	180	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.95	95.34	0.89	0.84	5	-
GCF_001244995.1	s__Intestinimonas massiliensis	78.7387	178	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	99.15	98.60	0.93	0.82	6	-
GCF_002159265.1	s__Flavonifractor sp002159265	78.6506	199	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773995.1	s__Dysosmobacter sp009773995	78.5669	213	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	99.84	99.84	0.82	0.82	2	-
GCA_019117605.1	s__Intestinimonas stercoravium	77.9875	154	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_910585265.1	s__Enterenecus sp910585265	77.8903	145	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018374635.1	s__An92 sp018374635	77.8781	164	941	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,168] [INFO] GTDB search result was written to GCF_014334055.1_ASM1433405v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:48,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:48,171] [INFO] DFAST_QC result json was written to GCF_014334055.1_ASM1433405v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:48,172] [INFO] DFAST_QC completed!
[2024-01-24 13:50:48,172] [INFO] Total running time: 0h0m53s