[2023-06-04 20:55:00,676] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:55:00,679] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:55:00,680] [INFO] DQC Reference Directory: /var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference
[2023-06-04 20:55:03,019] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:55:03,020] [INFO] Task started: Prodigal
[2023-06-04 20:55:03,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a34d1cf-0b9e-4dd9-b6bc-44e99deae1f8/GCA_934178665.1_ERR7738533_bin.83_genomic.fna.gz | prodigal -d GCA_934178665.1_ERR7738533_bin.83_genomic.fna/cds.fna -a GCA_934178665.1_ERR7738533_bin.83_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:55:04,968] [INFO] Task succeeded: Prodigal
[2023-06-04 20:55:04,968] [INFO] Task started: HMMsearch
[2023-06-04 20:55:04,968] [INFO] Running command: hmmsearch --tblout GCA_934178665.1_ERR7738533_bin.83_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference/reference_markers.hmm GCA_934178665.1_ERR7738533_bin.83_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:55:05,196] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:55:05,198] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a34d1cf-0b9e-4dd9-b6bc-44e99deae1f8/GCA_934178665.1_ERR7738533_bin.83_genomic.fna.gz]
[2023-06-04 20:55:05,220] [INFO] Query marker FASTA was written to GCA_934178665.1_ERR7738533_bin.83_genomic.fna/markers.fasta
[2023-06-04 20:55:05,220] [INFO] Task started: Blastn
[2023-06-04 20:55:05,220] [INFO] Running command: blastn -query GCA_934178665.1_ERR7738533_bin.83_genomic.fna/markers.fasta -db /var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference/reference_markers.fasta -out GCA_934178665.1_ERR7738533_bin.83_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:55:06,194] [INFO] Task succeeded: Blastn
[2023-06-04 20:55:06,198] [INFO] Selected 24 target genomes.
[2023-06-04 20:55:06,198] [INFO] Target genome list was writen to GCA_934178665.1_ERR7738533_bin.83_genomic.fna/target_genomes.txt
[2023-06-04 20:55:06,268] [INFO] Task started: fastANI
[2023-06-04 20:55:06,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a34d1cf-0b9e-4dd9-b6bc-44e99deae1f8/GCA_934178665.1_ERR7738533_bin.83_genomic.fna.gz --refList GCA_934178665.1_ERR7738533_bin.83_genomic.fna/target_genomes.txt --output GCA_934178665.1_ERR7738533_bin.83_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:55:15,932] [INFO] Task succeeded: fastANI
[2023-06-04 20:55:15,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:55:15,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:55:15,935] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:55:15,936] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:55:15,936] [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
--------------------------------------------------------------------------------
[2023-06-04 20:55:15,938] [INFO] DFAST Taxonomy check result was written to GCA_934178665.1_ERR7738533_bin.83_genomic.fna/tc_result.tsv
[2023-06-04 20:55:15,939] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:55:15,939] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:55:15,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference/checkm_data
[2023-06-04 20:55:15,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:55:15,964] [INFO] Task started: CheckM
[2023-06-04 20:55:15,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934178665.1_ERR7738533_bin.83_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934178665.1_ERR7738533_bin.83_genomic.fna/checkm_input GCA_934178665.1_ERR7738533_bin.83_genomic.fna/checkm_result
[2023-06-04 20:55:30,211] [INFO] Task succeeded: CheckM
[2023-06-04 20:55:30,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:55:30,248] [INFO] ===== Completeness check finished =====
[2023-06-04 20:55:30,249] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:55:30,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934178665.1_ERR7738533_bin.83_genomic.fna/markers.fasta)
[2023-06-04 20:55:30,250] [INFO] Task started: Blastn
[2023-06-04 20:55:30,250] [INFO] Running command: blastn -query GCA_934178665.1_ERR7738533_bin.83_genomic.fna/markers.fasta -db /var/lib/cwl/stge492fc10-0b70-4a60-88f7-8b75f6e2841f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934178665.1_ERR7738533_bin.83_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:55:30,980] [INFO] Task succeeded: Blastn
[2023-06-04 20:55:30,986] [INFO] Selected 24 target genomes.
[2023-06-04 20:55:30,986] [INFO] Target genome list was writen to GCA_934178665.1_ERR7738533_bin.83_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:55:31,034] [INFO] Task started: fastANI
[2023-06-04 20:55:31,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a34d1cf-0b9e-4dd9-b6bc-44e99deae1f8/GCA_934178665.1_ERR7738533_bin.83_genomic.fna.gz --refList GCA_934178665.1_ERR7738533_bin.83_genomic.fna/target_genomes_gtdb.txt --output GCA_934178665.1_ERR7738533_bin.83_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:55:36,602] [INFO] Task succeeded: fastANI
[2023-06-04 20:55:36,620] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:55:36,620] [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_900542735.1	s__Scybalousia sp900542735	98.0347	327	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	98.00	97.98	0.84	0.82	4	conclusive
GCA_002493865.1	s__Scybalousia sp002493865	78.0014	65	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769695.1	s__UMGS995 sp900769695	77.8421	68	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584255.1	s__Scybalousia sp910584255	77.829	111	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543675.1	s__Scybalousia sp900543675	77.4425	95	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Scybalousia	95.0	97.87	97.87	0.85	0.85	2	-
GCA_910587725.1	s__MGBC162581 sp910587725	77.2178	50	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__MGBC162581	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801525.1	s__RUG14670 sp902801525	76.8259	69	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG14670	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432595.1	s__CAG-710 sp000432595	76.761	69	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-710	95.0	98.45	98.40	0.90	0.89	3	-
GCA_017941235.1	s__CAG-417 sp017941235	76.5258	67	437	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_017541325.1	s__RUG11788 sp017541325	76.4418	68	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477275.1	s__CAG-417 sp002477275	76.2108	56	437	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_017510225.1	s__Faecimonas sp017510225	76.023	52	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Faecimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017528315.1	s__RUG591 sp017528315	76.0152	55	437	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG591	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:55:36,622] [INFO] GTDB search result was written to GCA_934178665.1_ERR7738533_bin.83_genomic.fna/result_gtdb.tsv
[2023-06-04 20:55:36,622] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:55:36,626] [INFO] DFAST_QC result json was written to GCA_934178665.1_ERR7738533_bin.83_genomic.fna/dqc_result.json
[2023-06-04 20:55:36,626] [INFO] DFAST_QC completed!
[2023-06-04 20:55:36,626] [INFO] Total running time: 0h0m36s