[2024-01-24 10:58:06,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference
[2024-01-24 10:58:09,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,641] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ac0befb-a238-4b74-8578-d9f2d4558789/GCF_016765585.1_ASM1676558v1_genomic.fna.gz | prodigal -d GCF_016765585.1_ASM1676558v1_genomic.fna/cds.fna -a GCF_016765585.1_ASM1676558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:17,792] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:17,792] [INFO] Task started: HMMsearch
[2024-01-24 10:58:17,792] [INFO] Running command: hmmsearch --tblout GCF_016765585.1_ASM1676558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference/reference_markers.hmm GCF_016765585.1_ASM1676558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:18,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:18,164] [INFO] Found 6/6 markers.
[2024-01-24 10:58:18,216] [INFO] Query marker FASTA was written to GCF_016765585.1_ASM1676558v1_genomic.fna/markers.fasta
[2024-01-24 10:58:18,217] [INFO] Task started: Blastn
[2024-01-24 10:58:18,217] [INFO] Running command: blastn -query GCF_016765585.1_ASM1676558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference/reference_markers.fasta -out GCF_016765585.1_ASM1676558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:18,817] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:18,820] [INFO] Selected 29 target genomes.
[2024-01-24 10:58:18,821] [INFO] Target genome list was writen to GCF_016765585.1_ASM1676558v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:18,870] [INFO] Task started: fastANI
[2024-01-24 10:58:18,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac0befb-a238-4b74-8578-d9f2d4558789/GCF_016765585.1_ASM1676558v1_genomic.fna.gz --refList GCF_016765585.1_ASM1676558v1_genomic.fna/target_genomes.txt --output GCF_016765585.1_ASM1676558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:37,713] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:37,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:37,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:37,729] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:37,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:37,730] [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 swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	79.0203	434	1603	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	77.6803	264	1603	95	below_threshold
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	76.8546	140	1603	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	76.8075	130	1603	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.7944	162	1603	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	76.7917	203	1603	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_001623875.1	33954	33954	type	True	76.6717	176	1603	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	76.5646	166	1603	95	below_threshold
Clostridium polynesiense	strain=MS1	GCA_000820705.1	1325933	1325933	type	True	76.5549	89	1603	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_900129955.1	33954	33954	type	True	76.5341	173	1603	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.5058	131	1603	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.4951	190	1603	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	76.2962	145	1603	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	76.2359	139	1603	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	76.2316	138	1603	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	76.2281	122	1603	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	76.2223	140	1603	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	76.1937	146	1603	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	75.6757	121	1603	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	75.6018	120	1603	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:37,732] [INFO] DFAST Taxonomy check result was written to GCF_016765585.1_ASM1676558v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:37,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:37,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:37,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference/checkm_data
[2024-01-24 10:58:37,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:37,785] [INFO] Task started: CheckM
[2024-01-24 10:58:37,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765585.1_ASM1676558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765585.1_ASM1676558v1_genomic.fna/checkm_input GCF_016765585.1_ASM1676558v1_genomic.fna/checkm_result
[2024-01-24 10:59:08,610] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:08,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:08,632] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:08,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:08,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765585.1_ASM1676558v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:08,634] [INFO] Task started: Blastn
[2024-01-24 10:59:08,634] [INFO] Running command: blastn -query GCF_016765585.1_ASM1676558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc48570bf-ee87-458b-a3d4-d643cf25c8d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765585.1_ASM1676558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:09,487] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:09,492] [INFO] Selected 24 target genomes.
[2024-01-24 10:59:09,492] [INFO] Target genome list was writen to GCF_016765585.1_ASM1676558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:09,511] [INFO] Task started: fastANI
[2024-01-24 10:59:09,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ac0befb-a238-4b74-8578-d9f2d4558789/GCF_016765585.1_ASM1676558v1_genomic.fna.gz --refList GCF_016765585.1_ASM1676558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016765585.1_ASM1676558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:26,293] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:26,310] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:26,310] [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_016765585.1	s__F0540 sp016765585	100.0	1600	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000466585.1	s__F0540 sp000466585	88.0108	1230	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167505.1	s__F0540 sp900167505	77.7153	266	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_014193895.1	s__Clostridium_AR fungisolvens	76.9029	140	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019207025.1	s__Clostridium_AM sp019207025	76.8094	162	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016316925.1	s__Clostridium_AM aciditolerans	76.7904	203	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	95.27	95.27	0.80	0.80	2	-
GCF_001623875.1	s__Clostridium_AM magnum	76.6717	176	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000619945.1	s__Clostridium_AO lundense	76.552	167	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820705.1	s__Clostridium_AA polynesiense	76.5319	90	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.2542	127	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_000807255.1	s__Clostridium_I pasteurianum	76.2281	122	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	99.98	99.90	1.00	0.99	7	-
GCF_000816675.1	s__Clostridium_J argentinense	76.2117	151	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.28	97.50	0.97	0.91	8	-
GCF_001405015.1	s__Clostridium disporicum	76.1629	91	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCA_015058525.1	s__Clostridium butyricum_A	76.1079	65	1603	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	76.0874	95	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCA_002455975.1	s__Clostridium_J sp002455975	76.048	134	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341865.1	s__Clostridium_J sp002341865	75.8753	146	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498355.1	s__Clostridium sp000498355	75.7817	114	1603	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	75.657	115	1603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:26,312] [INFO] GTDB search result was written to GCF_016765585.1_ASM1676558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:26,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:26,316] [INFO] DFAST_QC result json was written to GCF_016765585.1_ASM1676558v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:26,317] [INFO] DFAST_QC completed!
[2024-01-24 10:59:26,317] [INFO] Total running time: 0h1m20s