[2023-06-17 08:40:17,011] [INFO] DFAST_QC pipeline started.
[2023-06-17 08:40:17,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 08:40:17,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference
[2023-06-17 08:40:18,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 08:40:18,270] [INFO] Task started: Prodigal
[2023-06-17 08:40:18,271] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd476f8c-c0e1-41f0-849b-027d6d043255/GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna.gz | prodigal -d GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/cds.fna -a GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 08:40:22,875] [INFO] Task succeeded: Prodigal
[2023-06-17 08:40:22,875] [INFO] Task started: HMMsearch
[2023-06-17 08:40:22,875] [INFO] Running command: hmmsearch --tblout GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference/reference_markers.hmm GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/protein.faa > /dev/null
[2023-06-17 08:40:23,114] [INFO] Task succeeded: HMMsearch
[2023-06-17 08:40:23,115] [INFO] Found 6/6 markers.
[2023-06-17 08:40:23,145] [INFO] Query marker FASTA was written to GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/markers.fasta
[2023-06-17 08:40:23,146] [INFO] Task started: Blastn
[2023-06-17 08:40:23,146] [INFO] Running command: blastn -query GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/markers.fasta -db /var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference/reference_markers.fasta -out GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:40:23,829] [INFO] Task succeeded: Blastn
[2023-06-17 08:40:23,833] [INFO] Selected 15 target genomes.
[2023-06-17 08:40:23,834] [INFO] Target genome list was writen to GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/target_genomes.txt
[2023-06-17 08:40:23,840] [INFO] Task started: fastANI
[2023-06-17 08:40:23,840] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd476f8c-c0e1-41f0-849b-027d6d043255/GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna.gz --refList GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/target_genomes.txt --output GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 08:40:35,278] [INFO] Task succeeded: fastANI
[2023-06-17 08:40:35,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 08:40:35,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 08:40:35,282] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 08:40:35,282] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 08:40:35,282] [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
--------------------------------------------------------------------------------
[2023-06-17 08:40:35,285] [INFO] DFAST Taxonomy check result was written to GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/tc_result.tsv
[2023-06-17 08:40:35,285] [INFO] ===== Taxonomy check completed =====
[2023-06-17 08:40:35,285] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 08:40:35,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference/checkm_data
[2023-06-17 08:40:35,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 08:40:35,316] [INFO] Task started: CheckM
[2023-06-17 08:40:35,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/checkm_input GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/checkm_result
[2023-06-17 08:40:56,476] [INFO] Task succeeded: CheckM
[2023-06-17 08:40:56,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 08:40:56,504] [INFO] ===== Completeness check finished =====
[2023-06-17 08:40:56,505] [INFO] ===== Start GTDB Search =====
[2023-06-17 08:40:56,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/markers.fasta)
[2023-06-17 08:40:56,506] [INFO] Task started: Blastn
[2023-06-17 08:40:56,506] [INFO] Running command: blastn -query GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/markers.fasta -db /var/lib/cwl/stg404e77ef-0f1e-4635-8097-b41aab67e061/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 08:40:57,576] [INFO] Task succeeded: Blastn
[2023-06-17 08:40:57,581] [INFO] Selected 21 target genomes.
[2023-06-17 08:40:57,582] [INFO] Target genome list was writen to GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 08:40:57,609] [INFO] Task started: fastANI
[2023-06-17 08:40:57,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd476f8c-c0e1-41f0-849b-027d6d043255/GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna.gz --refList GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/target_genomes_gtdb.txt --output GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 08:41:05,253] [INFO] Task succeeded: fastANI
[2023-06-17 08:41:05,262] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 08:41:05,262] [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_900544985.1	s__UMGS731 sp900544985	100.0	572	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731	95.0	97.60	95.19	0.92	0.84	3	conclusive
GCA_017621475.1	s__UMGS731 sp017621475	77.7041	104	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017456005.1	s__UMGS731 sp017456005	77.3279	91	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731	95.0	97.90	97.90	0.91	0.91	2	-
GCA_015064725.1	s__UMGS731 sp015064725	77.1235	107	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463815.1	s__UMGS731 sp017463815	76.8337	82	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017451975.1	s__UMGS731 sp017451975	76.6694	88	626	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS731	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 08:41:05,264] [INFO] GTDB search result was written to GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/result_gtdb.tsv
[2023-06-17 08:41:05,265] [INFO] ===== GTDB Search completed =====
[2023-06-17 08:41:05,268] [INFO] DFAST_QC result json was written to GCA_905207685.1_ERR414233-mag-bin.24_genomic.fna/dqc_result.json
[2023-06-17 08:41:05,268] [INFO] DFAST_QC completed!
[2023-06-17 08:41:05,268] [INFO] Total running time: 0h0m48s