[2023-06-28 07:34:11,840] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:34:11,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:34:11,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference
[2023-06-28 07:34:13,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:34:13,058] [INFO] Task started: Prodigal
[2023-06-28 07:34:13,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c429535-cb6e-4c07-a4bf-0f6ff571ea67/GCA_944387535.1_BRZ_FR_bin67_genomic.fna.gz | prodigal -d GCA_944387535.1_BRZ_FR_bin67_genomic.fna/cds.fna -a GCA_944387535.1_BRZ_FR_bin67_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:34:15,326] [INFO] Task succeeded: Prodigal
[2023-06-28 07:34:15,326] [INFO] Task started: HMMsearch
[2023-06-28 07:34:15,326] [INFO] Running command: hmmsearch --tblout GCA_944387535.1_BRZ_FR_bin67_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference/reference_markers.hmm GCA_944387535.1_BRZ_FR_bin67_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:34:15,485] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:34:15,487] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8c429535-cb6e-4c07-a4bf-0f6ff571ea67/GCA_944387535.1_BRZ_FR_bin67_genomic.fna.gz]
[2023-06-28 07:34:15,504] [INFO] Query marker FASTA was written to GCA_944387535.1_BRZ_FR_bin67_genomic.fna/markers.fasta
[2023-06-28 07:34:15,504] [INFO] Task started: Blastn
[2023-06-28 07:34:15,504] [INFO] Running command: blastn -query GCA_944387535.1_BRZ_FR_bin67_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference/reference_markers.fasta -out GCA_944387535.1_BRZ_FR_bin67_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:34:16,061] [INFO] Task succeeded: Blastn
[2023-06-28 07:34:16,076] [INFO] Selected 25 target genomes.
[2023-06-28 07:34:16,077] [INFO] Target genome list was writen to GCA_944387535.1_BRZ_FR_bin67_genomic.fna/target_genomes.txt
[2023-06-28 07:34:16,078] [INFO] Task started: fastANI
[2023-06-28 07:34:16,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c429535-cb6e-4c07-a4bf-0f6ff571ea67/GCA_944387535.1_BRZ_FR_bin67_genomic.fna.gz --refList GCA_944387535.1_BRZ_FR_bin67_genomic.fna/target_genomes.txt --output GCA_944387535.1_BRZ_FR_bin67_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:34:27,772] [INFO] Task succeeded: fastANI
[2023-06-28 07:34:27,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:34:27,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:34:27,778] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:34:27,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 07:34:27,778] [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 neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	74.8439	50	473	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	74.8349	51	473	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	74.7541	56	473	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	74.7429	50	473	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:34:27,780] [INFO] DFAST Taxonomy check result was written to GCA_944387535.1_BRZ_FR_bin67_genomic.fna/tc_result.tsv
[2023-06-28 07:34:27,781] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:34:27,781] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:34:27,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference/checkm_data
[2023-06-28 07:34:27,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:34:27,799] [INFO] Task started: CheckM
[2023-06-28 07:34:27,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944387535.1_BRZ_FR_bin67_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944387535.1_BRZ_FR_bin67_genomic.fna/checkm_input GCA_944387535.1_BRZ_FR_bin67_genomic.fna/checkm_result
[2023-06-28 07:34:41,974] [INFO] Task succeeded: CheckM
[2023-06-28 07:34:41,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:34:41,991] [INFO] ===== Completeness check finished =====
[2023-06-28 07:34:41,991] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:34:41,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944387535.1_BRZ_FR_bin67_genomic.fna/markers.fasta)
[2023-06-28 07:34:41,992] [INFO] Task started: Blastn
[2023-06-28 07:34:41,992] [INFO] Running command: blastn -query GCA_944387535.1_BRZ_FR_bin67_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d16df14-5377-42b6-80c7-273e1b24bb93/dqc_reference/reference_markers_gtdb.fasta -out GCA_944387535.1_BRZ_FR_bin67_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:34:42,720] [INFO] Task succeeded: Blastn
[2023-06-28 07:34:42,724] [INFO] Selected 13 target genomes.
[2023-06-28 07:34:42,724] [INFO] Target genome list was writen to GCA_944387535.1_BRZ_FR_bin67_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:34:42,726] [INFO] Task started: fastANI
[2023-06-28 07:34:42,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c429535-cb6e-4c07-a4bf-0f6ff571ea67/GCA_944387535.1_BRZ_FR_bin67_genomic.fna.gz --refList GCA_944387535.1_BRZ_FR_bin67_genomic.fna/target_genomes_gtdb.txt --output GCA_944387535.1_BRZ_FR_bin67_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:34:45,966] [INFO] Task succeeded: fastANI
[2023-06-28 07:34:45,977] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 07:34:45,978] [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_905213875.1	s__CAG-269 sp905213875	80.518	239	473	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_900554565.1	s__CAG-269 sp900554565	80.4357	225	473	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_900554365.1	s__CAG-269 sp900554365	80.376	223	473	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_900762425.1	s__CAG-269 sp900762425	80.2969	250	473	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_014846485.1	s__CAG-269 sp014846485	80.0656	219	473	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_000431335.1	s__CAG-269 sp000431335	79.8956	221	473	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	79.741	154	473	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	79.2298	174	473	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_017410505.1	s__CAG-269 sp017410505	78.6024	162	473	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_017434295.1	s__CAG-269 sp017434295	77.9621	139	473	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_900752335.1	s__CAG-273 sp900752335	77.0675	94	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.80	98.80	0.79	0.79	2	-
GCA_017470645.1	s__CAG-492 sp017470645	76.9027	70	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002633185.1	s__CAG-492 sp002633185	76.8164	76	473	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 07:34:45,979] [INFO] GTDB search result was written to GCA_944387535.1_BRZ_FR_bin67_genomic.fna/result_gtdb.tsv
[2023-06-28 07:34:45,980] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:34:45,982] [INFO] DFAST_QC result json was written to GCA_944387535.1_BRZ_FR_bin67_genomic.fna/dqc_result.json
[2023-06-28 07:34:45,983] [INFO] DFAST_QC completed!
[2023-06-28 07:34:45,983] [INFO] Total running time: 0h0m34s