[2024-01-24 13:40:28,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference
[2024-01-24 13:40:31,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,144] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg8412acfe-0ed0-4560-9cd4-8325633a30c4/GCF_002234575.2_ASM223457v2_genomic.fna.gz | prodigal -d GCF_002234575.2_ASM223457v2_genomic.fna/cds.fna -a GCF_002234575.2_ASM223457v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:49,336] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:49,336] [INFO] Task started: HMMsearch
[2024-01-24 13:40:49,337] [INFO] Running command: hmmsearch --tblout GCF_002234575.2_ASM223457v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference/reference_markers.hmm GCF_002234575.2_ASM223457v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:49,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:49,714] [INFO] Found 6/6 markers.
[2024-01-24 13:40:49,765] [INFO] Query marker FASTA was written to GCF_002234575.2_ASM223457v2_genomic.fna/markers.fasta
[2024-01-24 13:40:49,765] [INFO] Task started: Blastn
[2024-01-24 13:40:49,765] [INFO] Running command: blastn -query GCF_002234575.2_ASM223457v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference/reference_markers.fasta -out GCF_002234575.2_ASM223457v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:50,419] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:50,423] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:50,423] [INFO] Target genome list was writen to GCF_002234575.2_ASM223457v2_genomic.fna/target_genomes.txt
[2024-01-24 13:40:50,430] [INFO] Task started: fastANI
[2024-01-24 13:40:50,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg8412acfe-0ed0-4560-9cd4-8325633a30c4/GCF_002234575.2_ASM223457v2_genomic.fna.gz --refList GCF_002234575.2_ASM223457v2_genomic.fna/target_genomes.txt --output GCF_002234575.2_ASM223457v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,120] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,132] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:05,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,132] [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
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	100.0	2204	2204	95	conclusive
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	99.9938	2203	2204	95	conclusive
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	99.9676	2142	2204	95	conclusive
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	91.3169	1226	2204	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	91.2391	1249	2204	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	91.1928	1248	2204	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	85.0299	179	2204	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	80.5276	250	2204	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	80.0203	139	2204	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.1233	431	2204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,134] [INFO] DFAST Taxonomy check result was written to GCF_002234575.2_ASM223457v2_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,135] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,135] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference/checkm_data
[2024-01-24 13:41:05,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:05,195] [INFO] Task started: CheckM
[2024-01-24 13:41:05,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002234575.2_ASM223457v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002234575.2_ASM223457v2_genomic.fna/checkm_input GCF_002234575.2_ASM223457v2_genomic.fna/checkm_result
[2024-01-24 13:42:00,484] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:00,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,514] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:00,515] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:00,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002234575.2_ASM223457v2_genomic.fna/markers.fasta)
[2024-01-24 13:42:00,516] [INFO] Task started: Blastn
[2024-01-24 13:42:00,516] [INFO] Running command: blastn -query GCF_002234575.2_ASM223457v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ac3412-9670-4fad-8eb6-c42e0123c198/dqc_reference/reference_markers_gtdb.fasta -out GCF_002234575.2_ASM223457v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:01,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:01,627] [INFO] Selected 8 target genomes.
[2024-01-24 13:42:01,627] [INFO] Target genome list was writen to GCF_002234575.2_ASM223457v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:01,635] [INFO] Task started: fastANI
[2024-01-24 13:42:01,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg8412acfe-0ed0-4560-9cd4-8325633a30c4/GCF_002234575.2_ASM223457v2_genomic.fna.gz --refList GCF_002234575.2_ASM223457v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002234575.2_ASM223457v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:12,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:12,209] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:12,209] [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_002234575.2	s__Enterocloster bolteae	100.0	2204	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	conclusive
GCF_000424325.1	s__Enterocloster clostridioformis_A	91.7077	1050	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCF_900113155.1	s__Enterocloster clostridioformis	91.3169	1226	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	-
GCF_005845215.1	s__Enterocloster sp005845215	88.3874	1514	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCA_000155435.1	s__Enterocloster sp000155435	81.3831	790	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
GCF_003434055.1	s__Enterocloster aldenensis	80.6676	765	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.16	97.51	0.89	0.78	13	-
GCF_000233455.1	s__Enterocloster citroniae	80.5954	764	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	77.7034	223	2204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,214] [INFO] GTDB search result was written to GCF_002234575.2_ASM223457v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:12,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:12,218] [INFO] DFAST_QC result json was written to GCF_002234575.2_ASM223457v2_genomic.fna/dqc_result.json
[2024-01-24 13:42:12,218] [INFO] DFAST_QC completed!
[2024-01-24 13:42:12,219] [INFO] Total running time: 0h1m43s