[2023-06-05 09:56:35,818] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:56:35,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:56:35,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference
[2023-06-05 09:56:37,148] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:56:37,149] [INFO] Task started: Prodigal
[2023-06-05 09:56:37,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg610de22d-e2f7-400c-9c5b-a1fbafb8ec3f/GCA_934178005.1_ERR7745614_bin.54_genomic.fna.gz | prodigal -d GCA_934178005.1_ERR7745614_bin.54_genomic.fna/cds.fna -a GCA_934178005.1_ERR7745614_bin.54_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:56:39,142] [INFO] Task succeeded: Prodigal
[2023-06-05 09:56:39,142] [INFO] Task started: HMMsearch
[2023-06-05 09:56:39,142] [INFO] Running command: hmmsearch --tblout GCA_934178005.1_ERR7745614_bin.54_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference/reference_markers.hmm GCA_934178005.1_ERR7745614_bin.54_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:56:39,362] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:56:39,364] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg610de22d-e2f7-400c-9c5b-a1fbafb8ec3f/GCA_934178005.1_ERR7745614_bin.54_genomic.fna.gz]
[2023-06-05 09:56:39,384] [INFO] Query marker FASTA was written to GCA_934178005.1_ERR7745614_bin.54_genomic.fna/markers.fasta
[2023-06-05 09:56:39,384] [INFO] Task started: Blastn
[2023-06-05 09:56:39,385] [INFO] Running command: blastn -query GCA_934178005.1_ERR7745614_bin.54_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference/reference_markers.fasta -out GCA_934178005.1_ERR7745614_bin.54_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:56:40,049] [INFO] Task succeeded: Blastn
[2023-06-05 09:56:40,052] [INFO] Selected 28 target genomes.
[2023-06-05 09:56:40,053] [INFO] Target genome list was writen to GCA_934178005.1_ERR7745614_bin.54_genomic.fna/target_genomes.txt
[2023-06-05 09:56:40,056] [INFO] Task started: fastANI
[2023-06-05 09:56:40,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg610de22d-e2f7-400c-9c5b-a1fbafb8ec3f/GCA_934178005.1_ERR7745614_bin.54_genomic.fna.gz --refList GCA_934178005.1_ERR7745614_bin.54_genomic.fna/target_genomes.txt --output GCA_934178005.1_ERR7745614_bin.54_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:56:51,670] [INFO] Task succeeded: fastANI
[2023-06-05 09:56:51,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:56:51,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:56:51,675] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:56:51,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:56:51,676] [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 senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	74.6556	51	443	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:56:51,710] [INFO] DFAST Taxonomy check result was written to GCA_934178005.1_ERR7745614_bin.54_genomic.fna/tc_result.tsv
[2023-06-05 09:56:51,711] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:56:51,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:56:51,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference/checkm_data
[2023-06-05 09:56:51,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:56:51,734] [INFO] Task started: CheckM
[2023-06-05 09:56:51,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934178005.1_ERR7745614_bin.54_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934178005.1_ERR7745614_bin.54_genomic.fna/checkm_input GCA_934178005.1_ERR7745614_bin.54_genomic.fna/checkm_result
[2023-06-05 09:57:06,807] [INFO] Task succeeded: CheckM
[2023-06-05 09:57:06,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:57:06,827] [INFO] ===== Completeness check finished =====
[2023-06-05 09:57:06,827] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:57:06,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934178005.1_ERR7745614_bin.54_genomic.fna/markers.fasta)
[2023-06-05 09:57:06,828] [INFO] Task started: Blastn
[2023-06-05 09:57:06,828] [INFO] Running command: blastn -query GCA_934178005.1_ERR7745614_bin.54_genomic.fna/markers.fasta -db /var/lib/cwl/stg5af030a1-719d-4712-8c9e-23ad90091b23/dqc_reference/reference_markers_gtdb.fasta -out GCA_934178005.1_ERR7745614_bin.54_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:57:07,700] [INFO] Task succeeded: Blastn
[2023-06-05 09:57:07,704] [INFO] Selected 20 target genomes.
[2023-06-05 09:57:07,704] [INFO] Target genome list was writen to GCA_934178005.1_ERR7745614_bin.54_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:57:07,705] [INFO] Task started: fastANI
[2023-06-05 09:57:07,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg610de22d-e2f7-400c-9c5b-a1fbafb8ec3f/GCA_934178005.1_ERR7745614_bin.54_genomic.fna.gz --refList GCA_934178005.1_ERR7745614_bin.54_genomic.fna/target_genomes_gtdb.txt --output GCA_934178005.1_ERR7745614_bin.54_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:57:11,925] [INFO] Task succeeded: fastANI
[2023-06-05 09:57:11,942] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:57:11,943] [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_900547995.1	s__UMGS1045 sp900547995	97.2461	343	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1045	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016290195.1	s__UMGS1045 sp016290195	78.4042	137	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1045	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752905.1	s__UBA5026 sp900557305	77.4918	87	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	99.98	99.97	0.93	0.92	3	-
GCA_017461465.1	s__RGIG4266 sp017461465	77.3702	56	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550255.1	s__UBA5026 sp900550255	77.2707	92	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	98.55	98.27	0.87	0.84	3	-
GCA_902773675.1	s__RUG11890 sp902773675	76.7407	70	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11890	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550145.1	s__CAG-1193 sp900550145	76.6854	56	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1193	95.0	98.80	98.48	0.76	0.71	3	-
GCA_902801685.1	s__RUG12438 sp902801685	76.6448	64	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG12438	95.0	98.56	98.56	0.78	0.78	2	-
GCA_018716405.1	s__Faecisoma merdavium	76.5991	89	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	97.86	97.86	0.74	0.74	2	-
GCA_015059285.1	s__SIG208 sp015059285	76.5595	91	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016282155.1	s__RGIG4266 sp016282155	76.3735	64	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG4266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520435.1	s__JAAYOI01 sp012520435	76.3604	77	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017887425.1	s__Faecisoma sp017887425	76.3403	67	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525855.1	s__CAG-417 sp017525855	76.1301	54	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521575.1	s__DUPI01 sp012521575	75.9144	53	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__DUPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775285.1	s__CAG-1000 sp902775285	75.7269	54	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556025.1	s__CAG-1000 sp900556025	75.6363	57	443	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-1000	95.0	99.88	99.88	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-05 09:57:11,947] [INFO] GTDB search result was written to GCA_934178005.1_ERR7745614_bin.54_genomic.fna/result_gtdb.tsv
[2023-06-05 09:57:11,948] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:57:11,954] [INFO] DFAST_QC result json was written to GCA_934178005.1_ERR7745614_bin.54_genomic.fna/dqc_result.json
[2023-06-05 09:57:11,954] [INFO] DFAST_QC completed!
[2023-06-05 09:57:11,954] [INFO] Total running time: 0h0m36s