[2023-06-28 10:22:07,842] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:22:07,846] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:22:07,846] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference
[2023-06-28 10:22:10,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:22:10,424] [INFO] Task started: Prodigal
[2023-06-28 10:22:10,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg26ddee76-3fd9-4c1e-b041-715cc87fb6fd/GCA_944376135.1_E0_LS_bin20_genomic.fna.gz | prodigal -d GCA_944376135.1_E0_LS_bin20_genomic.fna/cds.fna -a GCA_944376135.1_E0_LS_bin20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:22:17,596] [INFO] Task succeeded: Prodigal
[2023-06-28 10:22:17,597] [INFO] Task started: HMMsearch
[2023-06-28 10:22:17,597] [INFO] Running command: hmmsearch --tblout GCA_944376135.1_E0_LS_bin20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference/reference_markers.hmm GCA_944376135.1_E0_LS_bin20_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:22:17,917] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:22:17,919] [INFO] Found 6/6 markers.
[2023-06-28 10:22:17,982] [INFO] Query marker FASTA was written to GCA_944376135.1_E0_LS_bin20_genomic.fna/markers.fasta
[2023-06-28 10:22:17,982] [INFO] Task started: Blastn
[2023-06-28 10:22:17,982] [INFO] Running command: blastn -query GCA_944376135.1_E0_LS_bin20_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference/reference_markers.fasta -out GCA_944376135.1_E0_LS_bin20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:19,565] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:19,569] [INFO] Selected 18 target genomes.
[2023-06-28 10:22:19,569] [INFO] Target genome list was writen to GCA_944376135.1_E0_LS_bin20_genomic.fna/target_genomes.txt
[2023-06-28 10:22:19,571] [INFO] Task started: fastANI
[2023-06-28 10:22:19,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ddee76-3fd9-4c1e-b041-715cc87fb6fd/GCA_944376135.1_E0_LS_bin20_genomic.fna.gz --refList GCA_944376135.1_E0_LS_bin20_genomic.fna/target_genomes.txt --output GCA_944376135.1_E0_LS_bin20_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:22:33,431] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:33,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:22:33,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:22:33,449] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:22:33,449] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:22:33,449] [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_002959675.1	208479	208479	type	True	77.3905	187	861	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	77.3544	212	861	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	77.3214	190	861	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	77.2974	214	861	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	77.2842	192	861	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.2766	192	861	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.2598	190	861	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	77.1454	71	861	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.1441	193	861	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	76.5144	120	861	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	75.2722	51	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:22:33,451] [INFO] DFAST Taxonomy check result was written to GCA_944376135.1_E0_LS_bin20_genomic.fna/tc_result.tsv
[2023-06-28 10:22:33,452] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:22:33,452] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:22:33,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference/checkm_data
[2023-06-28 10:22:33,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:22:33,496] [INFO] Task started: CheckM
[2023-06-28 10:22:33,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944376135.1_E0_LS_bin20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944376135.1_E0_LS_bin20_genomic.fna/checkm_input GCA_944376135.1_E0_LS_bin20_genomic.fna/checkm_result
[2023-06-28 10:23:00,352] [INFO] Task succeeded: CheckM
[2023-06-28 10:23:00,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:23:00,379] [INFO] ===== Completeness check finished =====
[2023-06-28 10:23:00,379] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:23:00,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944376135.1_E0_LS_bin20_genomic.fna/markers.fasta)
[2023-06-28 10:23:00,380] [INFO] Task started: Blastn
[2023-06-28 10:23:00,380] [INFO] Running command: blastn -query GCA_944376135.1_E0_LS_bin20_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbde3ce0-f328-45af-a2cd-884ac46e9dc6/dqc_reference/reference_markers_gtdb.fasta -out GCA_944376135.1_E0_LS_bin20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:23:01,225] [INFO] Task succeeded: Blastn
[2023-06-28 10:23:01,231] [INFO] Selected 18 target genomes.
[2023-06-28 10:23:01,231] [INFO] Target genome list was writen to GCA_944376135.1_E0_LS_bin20_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:23:01,267] [INFO] Task started: fastANI
[2023-06-28 10:23:01,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ddee76-3fd9-4c1e-b041-715cc87fb6fd/GCA_944376135.1_E0_LS_bin20_genomic.fna.gz --refList GCA_944376135.1_E0_LS_bin20_genomic.fna/target_genomes_gtdb.txt --output GCA_944376135.1_E0_LS_bin20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:23:14,087] [INFO] Task succeeded: fastANI
[2023-06-28 10:23:14,104] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:23:14,105] [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
GCA_019119575.1	s__Enterocloster excrementipullorum	85.4222	571	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.43	99.23	0.94	0.92	5	-
GCF_902364025.1	s__Enterocloster lavalensis	77.6154	213	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.58	98.12	0.90	0.83	6	-
GCA_018380885.1	s__Enterocloster sp900555905	77.5068	208	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	77.4879	162	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
GCF_002234575.2	s__Enterocloster bolteae	77.3215	190	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	-
GCA_900555045.1	s__Enterocloster sp900555045	77.309	186	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158075.1	s__Enterocloster asparagiformis	77.2875	215	861	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_900770345.1	s__Enterocloster sp900770345	77.2841	163	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424325.1	s__Enterocloster clostridioformis_A	77.1806	202	861	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	77.1462	192	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	-
GCA_000155435.1	s__Enterocloster sp000155435	77.1423	188	861	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_000233455.1	s__Enterocloster citroniae	77.0326	176	861	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_018715565.1	s__Ventrimonas merdavium	76.6804	104	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_019116745.1	s__Lachnoclostridium_A stercorigallinarum	76.4658	94	861	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_910577655.1	s__Ventrimonas sp910577655	76.3178	94	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:23:14,107] [INFO] GTDB search result was written to GCA_944376135.1_E0_LS_bin20_genomic.fna/result_gtdb.tsv
[2023-06-28 10:23:14,107] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:23:14,112] [INFO] DFAST_QC result json was written to GCA_944376135.1_E0_LS_bin20_genomic.fna/dqc_result.json
[2023-06-28 10:23:14,112] [INFO] DFAST_QC completed!
[2023-06-28 10:23:14,112] [INFO] Total running time: 0h1m6s