[2023-06-28 23:08:22,204] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:08:22,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:08:22,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference
[2023-06-28 23:08:23,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:08:23,651] [INFO] Task started: Prodigal
[2023-06-28 23:08:23,651] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd96413f-5133-46f0-bb52-c5d79dcde6ad/GCA_944387435.1_BRZ_DD_bin29_genomic.fna.gz | prodigal -d GCA_944387435.1_BRZ_DD_bin29_genomic.fna/cds.fna -a GCA_944387435.1_BRZ_DD_bin29_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:08:26,385] [INFO] Task succeeded: Prodigal
[2023-06-28 23:08:26,386] [INFO] Task started: HMMsearch
[2023-06-28 23:08:26,386] [INFO] Running command: hmmsearch --tblout GCA_944387435.1_BRZ_DD_bin29_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference/reference_markers.hmm GCA_944387435.1_BRZ_DD_bin29_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:08:26,608] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:08:26,610] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcd96413f-5133-46f0-bb52-c5d79dcde6ad/GCA_944387435.1_BRZ_DD_bin29_genomic.fna.gz]
[2023-06-28 23:08:26,629] [INFO] Query marker FASTA was written to GCA_944387435.1_BRZ_DD_bin29_genomic.fna/markers.fasta
[2023-06-28 23:08:26,629] [INFO] Task started: Blastn
[2023-06-28 23:08:26,629] [INFO] Running command: blastn -query GCA_944387435.1_BRZ_DD_bin29_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference/reference_markers.fasta -out GCA_944387435.1_BRZ_DD_bin29_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:08:27,224] [INFO] Task succeeded: Blastn
[2023-06-28 23:08:27,227] [INFO] Selected 17 target genomes.
[2023-06-28 23:08:27,228] [INFO] Target genome list was writen to GCA_944387435.1_BRZ_DD_bin29_genomic.fna/target_genomes.txt
[2023-06-28 23:08:27,229] [INFO] Task started: fastANI
[2023-06-28 23:08:27,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd96413f-5133-46f0-bb52-c5d79dcde6ad/GCA_944387435.1_BRZ_DD_bin29_genomic.fna.gz --refList GCA_944387435.1_BRZ_DD_bin29_genomic.fna/target_genomes.txt --output GCA_944387435.1_BRZ_DD_bin29_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:08:34,718] [INFO] Task succeeded: fastANI
[2023-06-28 23:08:34,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:08:34,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:08:34,726] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:08:34,727] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:08:34,727] [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 fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	75.0106	51	534	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	74.9229	52	534	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	74.6916	65	534	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	74.6904	65	534	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:08:34,729] [INFO] DFAST Taxonomy check result was written to GCA_944387435.1_BRZ_DD_bin29_genomic.fna/tc_result.tsv
[2023-06-28 23:08:34,730] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:08:34,730] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:08:34,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference/checkm_data
[2023-06-28 23:08:34,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:08:34,766] [INFO] Task started: CheckM
[2023-06-28 23:08:34,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944387435.1_BRZ_DD_bin29_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944387435.1_BRZ_DD_bin29_genomic.fna/checkm_input GCA_944387435.1_BRZ_DD_bin29_genomic.fna/checkm_result
[2023-06-28 23:08:52,944] [INFO] Task succeeded: CheckM
[2023-06-28 23:08:52,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:08:52,969] [INFO] ===== Completeness check finished =====
[2023-06-28 23:08:52,969] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:08:52,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944387435.1_BRZ_DD_bin29_genomic.fna/markers.fasta)
[2023-06-28 23:08:52,970] [INFO] Task started: Blastn
[2023-06-28 23:08:52,970] [INFO] Running command: blastn -query GCA_944387435.1_BRZ_DD_bin29_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf1e4f84-7077-4540-b3c9-12efe0fa8aeb/dqc_reference/reference_markers_gtdb.fasta -out GCA_944387435.1_BRZ_DD_bin29_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:08:53,666] [INFO] Task succeeded: Blastn
[2023-06-28 23:08:53,671] [INFO] Selected 15 target genomes.
[2023-06-28 23:08:53,671] [INFO] Target genome list was writen to GCA_944387435.1_BRZ_DD_bin29_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:08:53,675] [INFO] Task started: fastANI
[2023-06-28 23:08:53,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd96413f-5133-46f0-bb52-c5d79dcde6ad/GCA_944387435.1_BRZ_DD_bin29_genomic.fna.gz --refList GCA_944387435.1_BRZ_DD_bin29_genomic.fna/target_genomes_gtdb.txt --output GCA_944387435.1_BRZ_DD_bin29_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:08:58,220] [INFO] Task succeeded: fastANI
[2023-06-28 23:08:58,233] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:08:58,233] [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_900762425.1	s__CAG-269 sp900762425	80.1987	268	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905213875.1	s__CAG-269 sp905213875	80.1243	279	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.16	98.07	0.72	0.64	3	-
GCA_014846485.1	s__CAG-269 sp014846485	80.0884	243	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554365.1	s__CAG-269 sp900554365	80.0596	226	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000431335.1	s__CAG-269 sp000431335	79.8644	241	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.17	98.64	0.90	0.86	6	-
GCA_900556695.1	s__CAG-269 sp900556695	79.846	155	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554565.1	s__CAG-269 sp900554565	79.716	231	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.93	97.94	0.90	0.85	3	-
GCA_900556945.1	s__CAG-269 sp900556945	79.5011	153	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.30	99.23	0.81	0.81	3	-
GCA_905215845.1	s__CAG-269 sp905215845	79.3061	143	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553985.1	s__CAG-269 sp900553985	79.2925	215	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.48	98.04	0.82	0.80	5	-
GCA_904387305.1	s__CAG-269 sp904387305	79.0255	238	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419495.1	s__CAG-269 sp904419495	78.8199	221	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551615.1	s__CAG-269 sp900551615	78.4347	196	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_000434335.1	s__CAG-492 sp000434335	77.0832	87	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	96.09	95.60	0.83	0.81	4	-
GCA_017528085.1	s__Scatovivens sp017528085	76.2785	65	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:08:58,235] [INFO] GTDB search result was written to GCA_944387435.1_BRZ_DD_bin29_genomic.fna/result_gtdb.tsv
[2023-06-28 23:08:58,236] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:08:58,239] [INFO] DFAST_QC result json was written to GCA_944387435.1_BRZ_DD_bin29_genomic.fna/dqc_result.json
[2023-06-28 23:08:58,239] [INFO] DFAST_QC completed!
[2023-06-28 23:08:58,240] [INFO] Total running time: 0h0m36s