[2024-01-25 20:17:07,420] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:07,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:07,422] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference
[2024-01-25 20:17:08,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:08,548] [INFO] Task started: Prodigal
[2024-01-25 20:17:08,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg29106aa2-4949-46ed-b1d8-313c02bf1b0b/GCF_030813415.1_ASM3081341v1_genomic.fna.gz | prodigal -d GCF_030813415.1_ASM3081341v1_genomic.fna/cds.fna -a GCF_030813415.1_ASM3081341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:12,658] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:12,658] [INFO] Task started: HMMsearch
[2024-01-25 20:17:12,658] [INFO] Running command: hmmsearch --tblout GCF_030813415.1_ASM3081341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference/reference_markers.hmm GCF_030813415.1_ASM3081341v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:12,932] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:12,934] [INFO] Found 6/6 markers.
[2024-01-25 20:17:12,965] [INFO] Query marker FASTA was written to GCF_030813415.1_ASM3081341v1_genomic.fna/markers.fasta
[2024-01-25 20:17:12,965] [INFO] Task started: Blastn
[2024-01-25 20:17:12,965] [INFO] Running command: blastn -query GCF_030813415.1_ASM3081341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference/reference_markers.fasta -out GCF_030813415.1_ASM3081341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:13,547] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:13,549] [INFO] Selected 20 target genomes.
[2024-01-25 20:17:13,550] [INFO] Target genome list was writen to GCF_030813415.1_ASM3081341v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:13,561] [INFO] Task started: fastANI
[2024-01-25 20:17:13,561] [INFO] Running command: fastANI --query /var/lib/cwl/stg29106aa2-4949-46ed-b1d8-313c02bf1b0b/GCF_030813415.1_ASM3081341v1_genomic.fna.gz --refList GCF_030813415.1_ASM3081341v1_genomic.fna/target_genomes.txt --output GCF_030813415.1_ASM3081341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:26,650] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:26,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:26,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:26,663] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:17:26,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:17:26,663] [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
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	92.4173	796	1086	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	82.8224	666	1086	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	78.6079	397	1086	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	78.505	405	1086	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.1192	315	1086	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.9152	266	1086	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.7977	322	1086	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	77.7945	319	1086	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.6678	285	1086	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.4047	288	1086	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.3656	312	1086	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.336	252	1086	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.3285	328	1086	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.3169	305	1086	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	77.2007	271	1086	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.1341	229	1086	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	77.1271	229	1086	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	77.1037	244	1086	95	below_threshold
Clostridium vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	77.0736	204	1086	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.299	152	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:26,665] [INFO] DFAST Taxonomy check result was written to GCF_030813415.1_ASM3081341v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:26,665] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:26,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:26,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference/checkm_data
[2024-01-25 20:17:26,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:26,702] [INFO] Task started: CheckM
[2024-01-25 20:17:26,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030813415.1_ASM3081341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030813415.1_ASM3081341v1_genomic.fna/checkm_input GCF_030813415.1_ASM3081341v1_genomic.fna/checkm_result
[2024-01-25 20:17:44,564] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:44,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:44,583] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:44,583] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:44,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030813415.1_ASM3081341v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:44,583] [INFO] Task started: Blastn
[2024-01-25 20:17:44,583] [INFO] Running command: blastn -query GCF_030813415.1_ASM3081341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7894c80-9e8e-4e97-92c3-4fe6fe6afb6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030813415.1_ASM3081341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:45,388] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:45,391] [INFO] Selected 11 target genomes.
[2024-01-25 20:17:45,391] [INFO] Target genome list was writen to GCF_030813415.1_ASM3081341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:45,398] [INFO] Task started: fastANI
[2024-01-25 20:17:45,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg29106aa2-4949-46ed-b1d8-313c02bf1b0b/GCF_030813415.1_ASM3081341v1_genomic.fna.gz --refList GCF_030813415.1_ASM3081341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030813415.1_ASM3081341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:52,468] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:52,476] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:17:52,476] [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_017873235.1	s__Clostridium moniliforme	92.4173	796	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907995.1	s__Clostridium sardiniense	82.8479	664	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498355.1	s__Clostridium sp000498355	81.6807	618	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789395.1	s__Clostridium baratii	81.0698	565	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCF_015234215.1	s__Clostridium sp015234215	78.6291	395	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002050515.1	s__Clostridium thermobutyricum	78.4814	408	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCF_002327185.1	s__Clostridium chauvoei	78.1656	311	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCA_017383505.1	s__Clostridium sp017383505	77.4058	130	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836325.1	s__Clostridium sp014836325	77.403	288	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290265.1	s__Clostridium cagae	77.3558	313	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCA_900540255.1	s__Clostridium sp900540255	77.3109	239	1086	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:52,477] [INFO] GTDB search result was written to GCF_030813415.1_ASM3081341v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:52,479] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:52,482] [INFO] DFAST_QC result json was written to GCF_030813415.1_ASM3081341v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:52,482] [INFO] DFAST_QC completed!
[2024-01-25 20:17:52,482] [INFO] Total running time: 0h0m45s