[2023-06-05 18:59:00,590] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:59:00,592] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:59:00,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference
[2023-06-05 18:59:01,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:59:01,842] [INFO] Task started: Prodigal
[2023-06-05 18:59:01,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgec94d22e-b74b-474e-831e-7835c25c096d/GCA_934293295.1_ERR7746411_bin.544_genomic.fna.gz | prodigal -d GCA_934293295.1_ERR7746411_bin.544_genomic.fna/cds.fna -a GCA_934293295.1_ERR7746411_bin.544_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:59:05,734] [INFO] Task succeeded: Prodigal
[2023-06-05 18:59:05,735] [INFO] Task started: HMMsearch
[2023-06-05 18:59:05,735] [INFO] Running command: hmmsearch --tblout GCA_934293295.1_ERR7746411_bin.544_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference/reference_markers.hmm GCA_934293295.1_ERR7746411_bin.544_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:59:06,007] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:59:06,009] [INFO] Found 6/6 markers.
[2023-06-05 18:59:06,039] [INFO] Query marker FASTA was written to GCA_934293295.1_ERR7746411_bin.544_genomic.fna/markers.fasta
[2023-06-05 18:59:06,039] [INFO] Task started: Blastn
[2023-06-05 18:59:06,040] [INFO] Running command: blastn -query GCA_934293295.1_ERR7746411_bin.544_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference/reference_markers.fasta -out GCA_934293295.1_ERR7746411_bin.544_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:06,593] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:06,598] [INFO] Selected 21 target genomes.
[2023-06-05 18:59:06,599] [INFO] Target genome list was writen to GCA_934293295.1_ERR7746411_bin.544_genomic.fna/target_genomes.txt
[2023-06-05 18:59:06,609] [INFO] Task started: fastANI
[2023-06-05 18:59:06,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgec94d22e-b74b-474e-831e-7835c25c096d/GCA_934293295.1_ERR7746411_bin.544_genomic.fna.gz --refList GCA_934293295.1_ERR7746411_bin.544_genomic.fna/target_genomes.txt --output GCA_934293295.1_ERR7746411_bin.544_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:59:17,968] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:17,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:59:17,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:59:17,970] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:59:17,971] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:59:17,971] [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
--------------------------------------------------------------------------------
[2023-06-05 18:59:17,973] [INFO] DFAST Taxonomy check result was written to GCA_934293295.1_ERR7746411_bin.544_genomic.fna/tc_result.tsv
[2023-06-05 18:59:17,974] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:59:17,975] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:59:17,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference/checkm_data
[2023-06-05 18:59:17,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:59:18,006] [INFO] Task started: CheckM
[2023-06-05 18:59:18,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934293295.1_ERR7746411_bin.544_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934293295.1_ERR7746411_bin.544_genomic.fna/checkm_input GCA_934293295.1_ERR7746411_bin.544_genomic.fna/checkm_result
[2023-06-05 18:59:36,988] [INFO] Task succeeded: CheckM
[2023-06-05 18:59:36,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:59:37,007] [INFO] ===== Completeness check finished =====
[2023-06-05 18:59:37,007] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:59:37,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934293295.1_ERR7746411_bin.544_genomic.fna/markers.fasta)
[2023-06-05 18:59:37,008] [INFO] Task started: Blastn
[2023-06-05 18:59:37,008] [INFO] Running command: blastn -query GCA_934293295.1_ERR7746411_bin.544_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d3cfb77-726f-4fa2-bb6c-72e0089b9493/dqc_reference/reference_markers_gtdb.fasta -out GCA_934293295.1_ERR7746411_bin.544_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:37,811] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:37,816] [INFO] Selected 15 target genomes.
[2023-06-05 18:59:37,817] [INFO] Target genome list was writen to GCA_934293295.1_ERR7746411_bin.544_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:59:37,820] [INFO] Task started: fastANI
[2023-06-05 18:59:37,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgec94d22e-b74b-474e-831e-7835c25c096d/GCA_934293295.1_ERR7746411_bin.544_genomic.fna.gz --refList GCA_934293295.1_ERR7746411_bin.544_genomic.fna/target_genomes_gtdb.txt --output GCA_934293295.1_ERR7746411_bin.544_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:59:42,979] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:42,990] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:59:42,991] [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_900767815.1	s__UBA10281 sp900767815	82.4562	340	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	96.63	96.03	0.81	0.74	3	-
GCA_900548285.1	s__UBA10281 sp900548285	82.0734	312	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	99.08	98.17	0.92	0.86	3	-
GCA_900764105.1	s__UBA10281 sp900764105	81.2743	240	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	97.70	97.70	0.79	0.79	2	-
GCA_000437515.1	s__UBA10281 sp000437515	78.8847	124	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	97.14	97.00	0.87	0.87	3	-
GCA_900767885.1	s__UBA10281 sp900767885	78.6818	125	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554485.1	s__UBA10281 sp900554485	78.0713	75	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	98.83	98.82	0.88	0.85	3	-
GCA_902797945.1	s__UBA10281 sp902797945	77.4294	77	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017479185.1	s__UBA10281 sp017479185	77.4176	66	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766475.1	s__UBA10281 sp902766475	77.3351	71	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	97.57	97.49	0.86	0.78	3	-
GCA_017466825.1	s__UBA10281 sp017466825	77.3052	56	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797515.1	s__UBA10281 sp902797515	77.0846	71	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017504655.1	s__UBA10281 sp017504655	76.9654	61	640	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA10281	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:59:42,993] [INFO] GTDB search result was written to GCA_934293295.1_ERR7746411_bin.544_genomic.fna/result_gtdb.tsv
[2023-06-05 18:59:42,993] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:59:42,996] [INFO] DFAST_QC result json was written to GCA_934293295.1_ERR7746411_bin.544_genomic.fna/dqc_result.json
[2023-06-05 18:59:42,997] [INFO] DFAST_QC completed!
[2023-06-05 18:59:42,997] [INFO] Total running time: 0h0m42s