[2023-06-28 13:28:36,678] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:28:36,685] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:28:36,685] [INFO] DQC Reference Directory: /var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference
[2023-06-28 13:28:37,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:28:37,850] [INFO] Task started: Prodigal
[2023-06-28 13:28:37,851] [INFO] Running command: gunzip -c /var/lib/cwl/stg459d9834-e555-490f-a974-a272d9fe2891/GCA_017886815.1_ASM1788681v1_genomic.fna.gz | prodigal -d GCA_017886815.1_ASM1788681v1_genomic.fna/cds.fna -a GCA_017886815.1_ASM1788681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:28:44,637] [INFO] Task succeeded: Prodigal
[2023-06-28 13:28:44,637] [INFO] Task started: HMMsearch
[2023-06-28 13:28:44,637] [INFO] Running command: hmmsearch --tblout GCA_017886815.1_ASM1788681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference/reference_markers.hmm GCA_017886815.1_ASM1788681v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:28:44,828] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:28:44,829] [INFO] Found 6/6 markers.
[2023-06-28 13:28:44,855] [INFO] Query marker FASTA was written to GCA_017886815.1_ASM1788681v1_genomic.fna/markers.fasta
[2023-06-28 13:28:44,855] [INFO] Task started: Blastn
[2023-06-28 13:28:44,855] [INFO] Running command: blastn -query GCA_017886815.1_ASM1788681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference/reference_markers.fasta -out GCA_017886815.1_ASM1788681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:28:45,497] [INFO] Task succeeded: Blastn
[2023-06-28 13:28:45,501] [INFO] Selected 19 target genomes.
[2023-06-28 13:28:45,501] [INFO] Target genome list was writen to GCA_017886815.1_ASM1788681v1_genomic.fna/target_genomes.txt
[2023-06-28 13:28:45,502] [INFO] Task started: fastANI
[2023-06-28 13:28:45,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg459d9834-e555-490f-a974-a272d9fe2891/GCA_017886815.1_ASM1788681v1_genomic.fna.gz --refList GCA_017886815.1_ASM1788681v1_genomic.fna/target_genomes.txt --output GCA_017886815.1_ASM1788681v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:28:56,777] [INFO] Task succeeded: fastANI
[2023-06-28 13:28:56,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:28:56,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:28:56,788] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:28:56,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:28:56,788] [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 asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.8526	231	847	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.8081	232	847	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	76.8437	79	847	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.8354	111	847	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.79	110	847	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.6944	109	847	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.6704	60	847	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.3098	107	847	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.2724	108	847	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.2683	108	847	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:28:56,790] [INFO] DFAST Taxonomy check result was written to GCA_017886815.1_ASM1788681v1_genomic.fna/tc_result.tsv
[2023-06-28 13:28:56,790] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:28:56,791] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:28:56,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference/checkm_data
[2023-06-28 13:28:56,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:28:56,821] [INFO] Task started: CheckM
[2023-06-28 13:28:56,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017886815.1_ASM1788681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017886815.1_ASM1788681v1_genomic.fna/checkm_input GCA_017886815.1_ASM1788681v1_genomic.fna/checkm_result
[2023-06-28 13:29:22,006] [INFO] Task succeeded: CheckM
[2023-06-28 13:29:22,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 13:29:22,026] [INFO] ===== Completeness check finished =====
[2023-06-28 13:29:22,026] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:29:22,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017886815.1_ASM1788681v1_genomic.fna/markers.fasta)
[2023-06-28 13:29:22,027] [INFO] Task started: Blastn
[2023-06-28 13:29:22,027] [INFO] Running command: blastn -query GCA_017886815.1_ASM1788681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40eefd32-377a-4867-bdc8-1f6247d70363/dqc_reference/reference_markers_gtdb.fasta -out GCA_017886815.1_ASM1788681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:29:23,085] [INFO] Task succeeded: Blastn
[2023-06-28 13:29:23,089] [INFO] Selected 14 target genomes.
[2023-06-28 13:29:23,089] [INFO] Target genome list was writen to GCA_017886815.1_ASM1788681v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:29:23,091] [INFO] Task started: fastANI
[2023-06-28 13:29:23,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg459d9834-e555-490f-a974-a272d9fe2891/GCA_017886815.1_ASM1788681v1_genomic.fna.gz --refList GCA_017886815.1_ASM1788681v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017886815.1_ASM1788681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:29:32,499] [INFO] Task succeeded: fastANI
[2023-06-28 13:29:32,511] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:29:32,511] [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_002160755.1	s__Lachnoclostridium_A sp002160755	98.3213	776	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	conclusive
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	81.6031	392	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_019114465.1	s__Lachnoclostridium_A avicola	81.1157	469	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.23	98.89	0.92	0.90	3	-
GCA_019119775.1	s__Lachnoclostridium_A pullistercoris	80.9232	432	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.96	99.96	0.95	0.95	2	-
GCA_019116745.1	s__Lachnoclostridium_A stercorigallinarum	80.6804	366	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.47	99.47	0.89	0.89	2	-
GCA_900555045.1	s__Enterocloster sp900555045	78.0768	212	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	77.9349	206	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCF_000158075.1	s__Enterocloster asparagiformis	77.8652	230	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCA_018223415.1	s__Copromonas sp900541255	77.0738	158	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	99.81	99.68	0.96	0.93	4	-
GCA_910575585.1	s__UBA3402 sp910575585	76.9985	121	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	99.89	99.85	0.96	0.96	3	-
GCA_900549235.1	s__Enterocloster sp900549235	76.9227	122	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.03	99.00	0.79	0.77	3	-
GCF_904420245.1	s__Paralachnospira avium	76.8217	81	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003464085.1	s__Lachnoclostridium_A sp003464085	76.6418	72	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005845215.1	s__Enterocloster sp005845215	76.5927	115	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
--------------------------------------------------------------------------------
[2023-06-28 13:29:32,515] [INFO] GTDB search result was written to GCA_017886815.1_ASM1788681v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:29:32,516] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:29:32,519] [INFO] DFAST_QC result json was written to GCA_017886815.1_ASM1788681v1_genomic.fna/dqc_result.json
[2023-06-28 13:29:32,520] [INFO] DFAST_QC completed!
[2023-06-28 13:29:32,520] [INFO] Total running time: 0h0m56s